rs4981283

Variant names:

• chr14-35340878-A-G
• rs4981283

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 0.505 in 152,024 control chromosomes in the GnomAD database, including 19,684 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 0.51 (19684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.505 AC: 76767 AN: 151906 Hom.: 19671 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.505 AC: 76825 AN: 152024 Hom.: 19684 Cov.: 32 AF XY: 0.509 AC XY: 37851 AN XY: 74298

African (AFR) AF: 0.444 AC: 18421 AN: 41476

American (AMR) AF: 0.501 AC: 7656 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3468

East Asian (EAS) AF: 0.687 AC: 3540 AN: 5154

South Asian (SAS) AF: 0.537 AC: 2589 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5818 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35658 AN: 67950

Other (OTH) AF: 0.499 AC: 1050 AN: 2106

Alfa AF: 0.513 Hom.: 12448

Bravo AF: 0.496

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.66
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs4981283; hg19: chr14-35810084;