11-48261740-A-T

Variant names:

• chr11-48261740-A-T
• rs7106648

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 0.69 in 152,060 control chromosomes in the GnomAD database, including 36,948 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 (36948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 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: 0.690 AC: 104824 AN: 151942 Hom.: 36935 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.690 AC: 104875 AN: 152060 Hom.: 36948 Cov.: 32 AF XY: 0.689 AC XY: 51231 AN XY: 74346

African (AFR) AF: 0.559 AC: 23180 AN: 41460

American (AMR) AF: 0.737 AC: 11253 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2406 AN: 3468

East Asian (EAS) AF: 0.578 AC: 2987 AN: 5172

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4826

European-Finnish (FIN) AF: 0.811 AC: 8595 AN: 10592

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51426 AN: 67962

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.730 Hom.: 5125

Bravo AF: 0.682

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.71
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7106648; hg19: chr11-48283292;