chr11-76590331-C-T

Variant names:

• chr11-76590331-C-T
• rs7927997

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 0.335 in 152,022 control chromosomes in the GnomAD database, including 8,756 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 0.33 (8756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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: 0.335 AC: 50872 AN: 151904 Hom.: 8757 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.335 AC: 50885 AN: 152022 Hom.: 8756 Cov.: 32 AF XY: 0.328 AC XY: 24402 AN XY: 74326

African (AFR) AF: 0.291 AC: 12073 AN: 41448

American (AMR) AF: 0.282 AC: 4319 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3468

East Asian (EAS) AF: 0.186 AC: 962 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1408 AN: 4810

European-Finnish (FIN) AF: 0.291 AC: 3077 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26042 AN: 67942

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.365 Hom.: 42364

Bravo AF: 0.335

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.61
DANN	Benign	0.60
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7927997; hg19: chr11-76301375;