chr14-94896415-G-C

Variant names:

• chr14-94896415-G-C
• rs1341002

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 0.622 in 152,020 control chromosomes in the GnomAD database, including 30,582 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 0.62 (30582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 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: 0.621 AC: 94398 AN: 151902 Hom.: 30535 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.622 AC: 94505 AN: 152020 Hom.: 30582 Cov.: 32 AF XY: 0.617 AC XY: 45832 AN XY: 74312

African (AFR) AF: 0.739 AC: 30662 AN: 41464

American (AMR) AF: 0.456 AC: 6967 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1388 AN: 5158

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4812

European-Finnish (FIN) AF: 0.697 AC: 7364 AN: 10568

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42026 AN: 67954

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.550 Hom.: 1816

Bravo AF: 0.607

Asia WGS AF: 0.418 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.48
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1341002; hg19: chr14-95362752;