14-95085217-T-C

Variant names:

• chr14-95085217-T-C
• rs1187650

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 0.774 in 152,158 control chromosomes in the GnomAD database, including 45,941 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 0.77 (45941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.774 AC: 117722 AN: 152040 Hom.: 45921 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.774 AC: 117792 AN: 152158 Hom.: 45941 Cov.: 32 AF XY: 0.779 AC XY: 57944 AN XY: 74388

African (AFR) AF: 0.686 AC: 28453 AN: 41506

American (AMR) AF: 0.838 AC: 12818 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2532 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4968 AN: 5180

South Asian (SAS) AF: 0.919 AC: 4439 AN: 4830

European-Finnish (FIN) AF: 0.775 AC: 8199 AN: 10578

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53865 AN: 67982

Other (OTH) AF: 0.763 AC: 1609 AN: 2108

Alfa AF: 0.785 Hom.: 64737

Bravo AF: 0.773

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1187650; hg19: chr14-95551554;