11-67577970-T-C

Variant names:

• chr11-67577970-T-C
• rs612020

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 0.887 in 152,222 control chromosomes in the GnomAD database, including 59,973 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 0.89 (59973 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 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: 0.887 AC: 134922 AN: 152104 Hom.: 59951 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.887 AC: 135000 AN: 152222 Hom.: 59973 Cov.: 33 AF XY: 0.886 AC XY: 65901 AN XY: 74418

African (AFR) AF: 0.842 AC: 34931 AN: 41510

American (AMR) AF: 0.892 AC: 13635 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4506 AN: 5176

South Asian (SAS) AF: 0.922 AC: 4452 AN: 4828

European-Finnish (FIN) AF: 0.839 AC: 8896 AN: 10606

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62405 AN: 68018

Other (OTH) AF: 0.899 AC: 1899 AN: 2112

Alfa AF: 0.888 Hom.: 8398

Bravo AF: 0.889

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs612020; hg19: chr11-67345441;