Variant rs2276919 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001395294.1(FAM149A):c.1602+174A>G variant causes a intron change. The variant allele was found at a frequency of 0.688 in 1,534,524 control chromosomes in the GnomAD database, including 366,389 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 0.65 ( 32362 hom., cov: 34)

Exomes 𝑓: 0.69 ( 334027 hom. )

Consequence

FAM149A
NM_001395294.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.37

Variant links:

Genes affected

FAM149A (HGNC:24527): (family with sequence similarity 149 member A)

FAM149A links:

RPSAP70 (HGNC:51923): (ribosomal protein SA pseudogene 70)

RPSAP70 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM149A	NM_001395294.1 linkuse as main transcript	c.1602+174A>G		intron_variant		ENST00000706927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM149A	ENST00000706927.1 linkuse as main transcript	c.1602+174A>G		intron_variant			NM_001395294.1	A2
RPSAP70	ENST00000504462.1 linkuse as main transcript			upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98543

AN:

152018

Hom.:

32342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.597

Gnomad EAS

AF:

0.565

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.656

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.632

GnomAD3 exomes

AF:

0.629

AC:

88317

AN:

140410

Hom.:

28287

AF XY:

0.638

AC XY:

48475

AN XY:

76022

show subpopulations

Gnomad AFR exome

AF:

0.595

Gnomad AMR exome

AF:

0.456

Gnomad ASJ exome

AF:

0.597

Gnomad EAS exome

AF:

0.579

Gnomad SAS exome

AF:

0.651

Gnomad FIN exome

AF:

0.659

Gnomad NFE exome

AF:

0.710

Gnomad OTH exome

AF:

0.638

GnomAD4 exome

AF:

0.693

AC:

957371

AN:

1382388

Hom.:

334027

Cov.:

AF XY:

0.691

AC XY:

471628

AN XY:

682428

show subpopulations

Gnomad4 AFR exome

AF:

0.594

Gnomad4 AMR exome

AF:

0.467

Gnomad4 ASJ exome

AF:

0.596

Gnomad4 EAS exome

AF:

0.537

Gnomad4 SAS exome

AF:

0.647

Gnomad4 FIN exome

AF:

0.662

Gnomad4 NFE exome

AF:

0.716

Gnomad4 OTH exome

AF:

0.669

GnomAD4 genome

AF:

0.648

AC:

98608

AN:

152136

Hom.:

32362

Cov.:

AF XY:

0.642

AC XY:

47739

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.600

Gnomad4 AMR

AF:

0.549

Gnomad4 ASJ

AF:

0.597

Gnomad4 EAS

AF:

0.565

Gnomad4 SAS

AF:

0.659

Gnomad4 FIN

AF:

0.656

Gnomad4 NFE

AF:

0.709

Gnomad4 OTH

AF:

0.629

Alfa

AF:

0.675

Hom.:

19705

Bravo

AF:

0.634

Asia WGS

AF:

0.625

AC:

2173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

4.5

DANN

Benign

0.58

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over