rs762009

chr14-35421655-A-Gchr14-35421655-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.718 in 152,104 control chromosomes in the GnomAD database, including 39,496 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 0.72 (39496 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109150 AN: 151986 Hom.: 39455 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.718 AC: 109242 AN: 152104 Hom.: 39496 Cov.: 31 AF XY: 0.714 AC XY: 53081 AN XY: 74334

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.699

Alfa AF: 0.721 Hom.: 19350

Bravo AF: 0.711

Asia WGS AF: 0.639 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762009; hg19: chr14-35890861;