11-76258705-T-C

Variant names:

• chr11-76258705-T-C
• rs4945056

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 0.761 in 151,958 control chromosomes in the GnomAD database, including 44,306 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 0.76 (44306 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 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: 0.761 AC: 115625 AN: 151840 Hom.: 44285 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.761 AC: 115683 AN: 151958 Hom.: 44306 Cov.: 30 AF XY: 0.751 AC XY: 55732 AN XY: 74254

African (AFR) AF: 0.732 AC: 30302 AN: 41388

American (AMR) AF: 0.719 AC: 10994 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3186 AN: 5160

South Asian (SAS) AF: 0.739 AC: 3557 AN: 4812

European-Finnish (FIN) AF: 0.657 AC: 6936 AN: 10558

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55214 AN: 67974

Other (OTH) AF: 0.773 AC: 1633 AN: 2112

Alfa AF: 0.797 Hom.: 135503

Bravo AF: 0.763

Asia WGS AF: 0.653 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4945056; hg19: chr11-75969749;