rs6760780

Variant names:

• chr2-189031312-T-A
• rs6760780

Your query was ambiguous. Multiple possible variants found:

• chr2-189031312-T-A
• chr2-189031312-T-C

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 0.796 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.564 AC: 23338 AN: 41374

American (AMR) AF: 0.785 AC: 11947 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3096 AN: 3466

East Asian (EAS) AF: 0.829 AC: 4269 AN: 5152

South Asian (SAS) AF: 0.824 AC: 3967 AN: 4814

European-Finnish (FIN) AF: 0.911 AC: 9658 AN: 10600

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.911 AC: 61925 AN: 67970

Other (OTH) AF: 0.802 AC: 1688 AN: 2106

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6760780; hg19: chr2-189896038;