14-99682624-T-C

Variant names:

• chr14-99682624-T-C
• rs8003602

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 0.673 in 151,980 control chromosomes in the GnomAD database, including 35,327 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 0.67 (35327 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 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: 0.673 AC: 102202 AN: 151862 Hom.: 35321 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.673 AC: 102247 AN: 151980 Hom.: 35327 Cov.: 31 AF XY: 0.676 AC XY: 50250 AN XY: 74282

African (AFR) AF: 0.513 AC: 21228 AN: 41392

American (AMR) AF: 0.686 AC: 10496 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2498 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3093 AN: 5148

South Asian (SAS) AF: 0.836 AC: 4024 AN: 4812

European-Finnish (FIN) AF: 0.739 AC: 7826 AN: 10590

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50703 AN: 67962

Other (OTH) AF: 0.675 AC: 1422 AN: 2108

Alfa AF: 0.662 Hom.: 15628

Bravo AF: 0.659

Asia WGS AF: 0.710 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs8003602; hg19: chr14-100148961;