7-116511101-T-C

Variant names:

• chr7-116511101-T-C
• rs6466579

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 0.491 in 151,836 control chromosomes in the GnomAD database, including 18,916 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 0.49 (18916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.491 AC: 74542 AN: 151718 Hom.: 18894 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.491 AC: 74606 AN: 151836 Hom.: 18916 Cov.: 31 AF XY: 0.499 AC XY: 37052 AN XY: 74206

African (AFR) AF: 0.391 AC: 16193 AN: 41390

American (AMR) AF: 0.560 AC: 8540 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3468

East Asian (EAS) AF: 0.773 AC: 4000 AN: 5174

South Asian (SAS) AF: 0.549 AC: 2642 AN: 4816

European-Finnish (FIN) AF: 0.566 AC: 5951 AN: 10520

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34017 AN: 67910

Other (OTH) AF: 0.502 AC: 1058 AN: 2108

Alfa AF: 0.489 Hom.: 39820

Bravo AF: 0.484

Asia WGS AF: 0.679 AC: 2356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.9
DANN	Benign	0.82
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6466579; hg19: chr7-116151155;