rs7758766

Variant names:

• chr6-160685476-G-T
• rs7758766

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 0.164 in 152,150 control chromosomes in the GnomAD database, including 2,172 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 0.16 (2172 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.164 AC: 24954 AN: 152030 Hom.: 2165 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00465

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.164 AC: 24983 AN: 152150 Hom.: 2172 Cov.: 33 AF XY: 0.159 AC XY: 11849 AN XY: 74386

African (AFR) AF: 0.212 AC: 8796 AN: 41522

American (AMR) AF: 0.142 AC: 2165 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.00466 AC: 24 AN: 5154

South Asian (SAS) AF: 0.118 AC: 570 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1211 AN: 10604

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11101 AN: 67966

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.161 Hom.: 220

Bravo AF: 0.167

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.0
DANN	Benign	0.95
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs7758766; hg19: chr6-161106508;