rs4902661

Variant names:

• chr14-68870464-C-T
• rs4902661

Variant summary

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

The variant allele was found at a frequency of 0.688 in 145,818 control chromosomes in the GnomAD database, including 34,782 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 0.69 (34782 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 100277 AN: 145770 Hom.: 34769 Cov.: 25

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.688 AC: 100304 AN: 145818 Hom.: 34782 Cov.: 25 AF XY: 0.688 AC XY: 48519 AN XY: 70528

African (AFR) AF: 0.673 AC: 26441 AN: 39306

American (AMR) AF: 0.768 AC: 11159 AN: 14528

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2507 AN: 3462

East Asian (EAS) AF: 0.498 AC: 2494 AN: 5010

South Asian (SAS) AF: 0.749 AC: 3522 AN: 4704

European-Finnish (FIN) AF: 0.644 AC: 5293 AN: 8220

Middle Eastern (MID) AF: 0.670 AC: 189 AN: 282

European-Non Finnish (NFE) AF: 0.692 AC: 46649 AN: 67366

Other (OTH) AF: 0.691 AC: 1409 AN: 2038

Alfa AF: 0.691 Hom.: 12547

Bravo AF: 0.695

Asia WGS AF: 0.696 AC: 2407 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4902661; hg19: chr14-69337181;