rs2276919

Positions:

• chr4-186157893-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.37

Genes affected

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

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

ACMG classification

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	c.1602+174A>G		intron_variant		ENST00000706927.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98543 AN: 152018 Hom.: 32342 Cov.: 34

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

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.: 35 AF XY: 0.691 AC XY: 471628 AN XY: 682428

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.: 34 AF XY: 0.642 AC XY: 47739 AN XY: 74362

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

Other links and lift over

dbSNP: rs2276919; hg19: chr4-187079047; COSMIC: COSV57025535; COSMIC: COSV57025535;