dbSNP rs2262274: FAM241B:c.96+112C>T (chr10-69631951-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145306.3(FAM241B):c.96+112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,912 control chromosomes in the GnomAD database, including 34,088 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 34088 hom., cov: 31)

Exomes 𝑓: 0.68 ( 296954 hom. )

Failed GnomAD Quality Control

Consequence

FAM241B
NM_145306.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727

Publications

1 publications found

Variant links:

Genes affected

FAM241B (HGNC:23519): (family with sequence similarity 241 member B) Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

FAM241B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FAM241B	NM_145306.3 link	c.96+112C>T	intron_variant	Intron 3 of 3	ENST00000373279.6	NP_660349.1	Q96D05-1A0A024QZL0
FAM241B	XM_005269606.3 link	c.222+112C>T	intron_variant	Intron 3 of 3		XP_005269663.1	Q96D05-2
FAM241B	XM_005269608.4 link	c.96+112C>T	intron_variant	Intron 2 of 2		XP_005269665.1	Q96D05-1A0A024QZL0
FAM241B	XM_011539455.3 link	c.96+112C>T	intron_variant	Intron 3 of 3		XP_011537757.1	Q96D05-1A0A024QZL0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FAM241B	ENST00000373279.6 link	c.96+112C>T	intron_variant	Intron 3 of 3	1	NM_145306.3	ENSP00000362376.4	Q96D05-1
FAM241B	ENST00000421716.1 link	c.222+112C>T	intron_variant	Intron 3 of 3	2		ENSP00000398621.1	Q5VVH9
FAM241B	ENST00000491890.1 link	n.423+112C>T	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.667

AC:

101190

AN:

151794

Hom.:

34051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.739

Gnomad ASJ

AF:

0.565

Gnomad EAS

AF:

0.895

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.662

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.681

AC:

864344

AN:

1269930

Hom.:

296954

AF XY:

0.680

AC XY:

425003

AN XY:

625360

show subpopulations

African (AFR)

AF:

0.624

AC:

17591

AN:

28204

American (AMR)

AF:

0.815

AC:

25491

AN:

31292

Ashkenazi Jewish (ASJ)

AF:

0.577

AC:

12701

AN:

22010

East Asian (EAS)

AF:

0.881

AC:

30651

AN:

34798

South Asian (SAS)

AF:

0.680

AC:

48594

AN:

71458

European-Finnish (FIN)

AF:

0.623

AC:

25259

AN:

40546

Middle Eastern (MID)

AF:

0.592

AC:

3077

AN:

5196

European-Non Finnish (NFE)

AF:

0.677

AC:

665482

AN:

983290

Other (OTH)

AF:

0.668

AC:

35498

AN:

53136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

12446

24892

37337

49783

62229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17326

34652

51978

69304

86630

<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:

0.667

AC:

101285

AN:

151912

Hom.:

34088

Cov.:

AF XY:

0.665

AC XY:

49392

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.630

AC:

26092

AN:

41448

American (AMR)

AF:

0.740

AC:

11301

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

1958

AN:

3466

East Asian (EAS)

AF:

0.895

AC:

4620

AN:

5164

South Asian (SAS)

AF:

0.679

AC:

3275

AN:

4820

European-Finnish (FIN)

AF:

0.607

AC:

6397

AN:

10546

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.672

AC:

45585

AN:

67880

Other (OTH)

AF:

0.660

AC:

1392

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1712

3424

5137

6849

8561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.653

Hom.:

4042

Bravo

AF:

0.679

Asia WGS

AF:

0.784

AC:

2725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.4

(source)

DANN

Benign

0.56

PhyloP100

-0.73

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over