rs6760780

chr2-189031312-T-Achr2-189031312-T-C

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 0.796 in 151,894 control chromosomes in the GnomAD database, including 49,793 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 0.80 (49793 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 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: 0.796 AC: 120871 AN: 151776 Hom.: 49785 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.796 AC: 120910 AN: 151894 Hom.: 49793 Cov.: 30 AF XY: 0.797 AC XY: 59158 AN XY: 74268

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.802

Alfa AF: 0.843 Hom.: 6867

Bravo AF: 0.774

Asia WGS AF: 0.774 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.1
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6760780; hg19: chr2-189896038;