Genetic Variant NM_182623.3:c.562+9C>T (chr1-16059485-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182623.3(FAM131C):c.562+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 1,599,760 control chromosomes in the GnomAD database, including 442,213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 36818 hom., cov: 32)

Exomes 𝑓: 0.75 ( 405395 hom. )

Consequence

FAM131C
NM_182623.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.210

Publications

10 publications found

Variant links:

Genes affected

FAM131C (HGNC:26717): (family with sequence similarity 131 member C)

FAM131C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-16059485-G-A is Benign according to our data. Variant chr1-16059485-G-A is described in ClinVar as Benign. ClinVar VariationId is 1287141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182623.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM131C	NM_182623.3	MANE Select	c.562+9C>T		intron	N/A	NP_872429.2	Q96AQ9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM131C	ENST00000375662.5	TSL:1 MANE Select	c.562+9C>T	intron	N/A	ENSP00000364814.4	Q96AQ9
FAM131C	ENST00000943020.1		c.526+9C>T	intron	N/A	ENSP00000613079.1
FAM131C	ENST00000904375.1		c.379+9C>T	intron	N/A	ENSP00000574434.1

Frequencies

GnomAD3 genomes

AF:

0.693

AC:

104757

AN:

151232

Hom.:

36809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.515

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.806

Gnomad ASJ

AF:

0.746

Gnomad EAS

AF:

0.822

Gnomad SAS

AF:

0.814

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.750

GnomAD2 exomes

AF:

0.749

AC:

178717

AN:

238550

AF XY:

0.752

show subpopulations

Gnomad AFR exome

AF:

0.494

Gnomad AMR exome

AF:

0.850

Gnomad ASJ exome

AF:

0.753

Gnomad EAS exome

AF:

0.814

Gnomad FIN exome

AF:

0.668

Gnomad NFE exome

AF:

0.746

Gnomad OTH exome

AF:

0.759

GnomAD4 exome

AF:

0.749

AC:

1085014

AN:

1448412

Hom.:

405395

Cov.:

AF XY:

0.752

AC XY:

540786

AN XY:

719458

show subpopulations

African (AFR)

AF:

0.493

AC:

16304

AN:

33040

American (AMR)

AF:

0.844

AC:

36410

AN:

43150

Ashkenazi Jewish (ASJ)

AF:

0.756

AC:

19402

AN:

25660

East Asian (EAS)

AF:

0.833

AC:

32741

AN:

39282

South Asian (SAS)

AF:

0.804

AC:

68089

AN:

84640

European-Finnish (FIN)

AF:

0.676

AC:

35437

AN:

52406

Middle Eastern (MID)

AF:

0.787

AC:

4491

AN:

5704

European-Non Finnish (NFE)

AF:

0.749

AC:

827575

AN:

1104716

Other (OTH)

AF:

0.745

AC:

44565

AN:

59814

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

Heterozygous variant carriers

13851

27702

41552

55403

69254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20280

40560

60840

81120

101400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.692

AC:

104804

AN:

151348

Hom.:

36818

Cov.:

AF XY:

0.694

AC XY:

51294

AN XY:

73916

show subpopulations

African (AFR)

AF:

0.515

AC:

21172

AN:

41142

American (AMR)

AF:

0.806

AC:

12256

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.746

AC:

2574

AN:

3452

East Asian (EAS)

AF:

0.823

AC:

4220

AN:

5128

South Asian (SAS)

AF:

0.814

AC:

3877

AN:

4762

European-Finnish (FIN)

AF:

0.679

AC:

7163

AN:

10556

Middle Eastern (MID)

AF:

0.782

AC:

230

AN:

294

European-Non Finnish (NFE)

AF:

0.753

AC:

51062

AN:

67802

Other (OTH)

AF:

0.750

AC:

1573

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1260

2520

3780

5040

6300

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.717

Hom.:

9412

Asia WGS

AF:

0.762

AC:

2649

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.016

(source)

DANN

Benign

0.74

PhyloP100

0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over