Genetic Variant NM_001029888.3:c.-69G>A (chr10-122910753-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001029888.3(FAM24A):c.-69G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,982 control chromosomes in the GnomAD database, including 18,679 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 0.49 ( 18677 hom., cov: 31)

Exomes 𝑓: 0.70 ( 2 hom. )

Consequence

FAM24A
NM_001029888.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.886

Publications

9 publications found

Variant links:

Genes affected

FAM24A (HGNC:23470): (family with sequence similarity 24 member A) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

FAM24A 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FAM24A	NM_001029888.3 link	c.-69G>A	5_prime_UTR_variant	Exon 1 of 3	ENST00000368894.2	NP_001025059.1	A6NFZ4
FAM24A	XM_017015638.2 link	c.-66G>A	5_prime_UTR_variant	Exon 1 of 3		XP_016871127.1	A6NFZ4
FAM24A	XM_017015639.2 link	c.-3+32G>A	intron_variant	Intron 1 of 2		XP_016871128.1	A6NFZ4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM24A	ENST00000368894.2 link	c.-69G>A		5_prime_UTR_variant	Exon 1 of 3	3	NM_001029888.3	ENSP00000357889.1		A6NFZ4

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74278

AN:

151850

Hom.:

18675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.625

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.490

GnomAD4 exome

AF:

0.700

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.489

AC:

74296

AN:

151972

Hom.:

18677

Cov.:

AF XY:

0.490

AC XY:

36433

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.396

AC:

16419

AN:

41436

American (AMR)

AF:

0.468

AC:

7163

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.495

AC:

1718

AN:

3468

East Asian (EAS)

AF:

0.424

AC:

2186

AN:

5150

South Asian (SAS)

AF:

0.462

AC:

2226

AN:

4822

European-Finnish (FIN)

AF:

0.625

AC:

6587

AN:

10544

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.533

AC:

36199

AN:

67954

Other (OTH)

AF:

0.489

AC:

1026

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1917

3834

5752

7669

9586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.491

Hom.:

2428

Bravo

AF:

0.471

Asia WGS

AF:

0.437

AC:

1519

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.92

(source)

DANN

Benign

0.42

PhyloP100

-0.89

PromoterAI

-0.0040

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over