rs960640

Variant names:

• chr11-48268768-A-G
• rs960640

Your query was ambiguous. Multiple possible variants found:

• chr11-48268768-A-G
• chr11-48268768-A-T

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 0.692 in 152,026 control chromosomes in the GnomAD database, including 37,144 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 0.69 (37144 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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: 0.692 AC: 105167 AN: 151908 Hom.: 37131 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.692 AC: 105221 AN: 152026 Hom.: 37144 Cov.: 31 AF XY: 0.691 AC XY: 51376 AN XY: 74302

African (AFR) AF: 0.567 AC: 23510 AN: 41464

American (AMR) AF: 0.738 AC: 11268 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2966 AN: 5148

South Asian (SAS) AF: 0.545 AC: 2629 AN: 4826

European-Finnish (FIN) AF: 0.811 AC: 8571 AN: 10566

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51461 AN: 67968

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.725 Hom.: 5035

Bravo AF: 0.685

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs960640; hg19: chr11-48290320;