rs7660462

Variant names:

• chr4-186138565-C-T
• rs7660462
• NM_001395294.1:c.567-10608C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395294.1(FAM149A):​c.567-10608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,928 control chromosomes in the GnomAD database, including 10,092 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 0.36 (10092 hom., cov: 31)
• Consequence: FAM149A NM_001395294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM149A	NM_001395294.1	c.567-10608C>T		intron_variant	Intron 1 of 13	ENST00000706927.1	NP_001382223.1
FAM149A	NM_001367768.3	c.567-10608C>T		intron_variant	Intron 1 of 13		NP_001354697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM149A	ENST00000706927.1	c.567-10608C>T		intron_variant	Intron 1 of 13		NM_001395294.1	ENSP00000516649.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54280 AN: 151810 Hom.: 10081 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.384

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 54317 AN: 151928 Hom.: 10092 Cov.: 31 AF XY: 0.353 AC XY: 26204 AN XY: 74248

African (AFR) AF: 0.272 AC: 11253 AN: 41424

American (AMR) AF: 0.391 AC: 5966 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1463 AN: 5154

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4816

European-Finnish (FIN) AF: 0.314 AC: 3314 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27517 AN: 67938

Other (OTH) AF: 0.388 AC: 819 AN: 2110

Alfa AF: 0.394 Hom.: 50849

Bravo AF: 0.362

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.84
PhyloP100		-2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7660462; hg19: chr4-187059719;