14-41256968-A-G

Variant names:

• chr14-41256968-A-G
• rs1782141

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 0.745 in 152,114 control chromosomes in the GnomAD database, including 42,453 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 0.75 (42453 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113284 AN: 151998 Hom.: 42411 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.745 AC: 113385 AN: 152114 Hom.: 42453 Cov.: 33 AF XY: 0.744 AC XY: 55345 AN XY: 74352

African (AFR) AF: 0.789 AC: 32737 AN: 41492

American (AMR) AF: 0.781 AC: 11955 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2711 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3667 AN: 5158

South Asian (SAS) AF: 0.651 AC: 3143 AN: 4826

European-Finnish (FIN) AF: 0.679 AC: 7176 AN: 10564

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49482 AN: 67986

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.752 Hom.: 5578

Bravo AF: 0.755

Asia WGS AF: 0.695 AC: 2416 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.47
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1782141; hg19: chr14-41726171;