rs4983382

Variant names:

• chr14-104723167-G-A
• rs4983382

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 0.818 in 152,198 control chromosomes in the GnomAD database, including 51,297 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 0.82 (51297 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.818 AC: 124398 AN: 152080 Hom.: 51251 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.818 AC: 124499 AN: 152198 Hom.: 51297 Cov.: 34 AF XY: 0.818 AC XY: 60892 AN XY: 74424

African (AFR) AF: 0.909 AC: 37779 AN: 41560

American (AMR) AF: 0.839 AC: 12843 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2798 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4755 AN: 5154

South Asian (SAS) AF: 0.737 AC: 3555 AN: 4822

European-Finnish (FIN) AF: 0.774 AC: 8193 AN: 10592

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51937 AN: 67984

Other (OTH) AF: 0.829 AC: 1748 AN: 2108

Alfa AF: 0.785 Hom.: 106594

Bravo AF: 0.831

Asia WGS AF: 0.850 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs4983382; hg19: chr14-105189504;