11-81772977-A-G

Variant names:

• chr11-81772977-A-G
• rs7106258

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 0.362 in 151,890 control chromosomes in the GnomAD database, including 10,526 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 0.36 (10526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54903 AN: 151774 Hom.: 10519 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.362 AC: 54944 AN: 151890 Hom.: 10526 Cov.: 31 AF XY: 0.361 AC XY: 26808 AN XY: 74236

African (AFR) AF: 0.486 AC: 20115 AN: 41352

American (AMR) AF: 0.281 AC: 4295 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3472

East Asian (EAS) AF: 0.188 AC: 973 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2322 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10540

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.321 AC: 21786 AN: 67968

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.333 Hom.: 5285

Bravo AF: 0.360

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs7106258; hg19: chr11-81484019;