chr14-40451205-G-C

Variant names:

• chr14-40451205-G-C
• rs2015019

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 0.478 in 151,832 control chromosomes in the GnomAD database, including 17,426 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 0.48 (17426 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.538 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: 0.477 AC: 72439 AN: 151714 Hom.: 17408 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.478 AC: 72505 AN: 151832 Hom.: 17426 Cov.: 31 AF XY: 0.476 AC XY: 35322 AN XY: 74200

African (AFR) AF: 0.433 AC: 17926 AN: 41366

American (AMR) AF: 0.548 AC: 8353 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3466

East Asian (EAS) AF: 0.410 AC: 2112 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2117 AN: 4810

European-Finnish (FIN) AF: 0.443 AC: 4660 AN: 10518

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33999 AN: 67952

Other (OTH) AF: 0.520 AC: 1097 AN: 2108

Alfa AF: 0.496 Hom.: 2339

Bravo AF: 0.485

Asia WGS AF: 0.466 AC: 1615 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	7.6
DANN	Benign	0.91
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2015019; hg19: chr14-40920409;