rs6928791

Variant names:

• chr6-148574216-G-A
• rs6928791

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 0.186 in 152,132 control chromosomes in the GnomAD database, including 2,888 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 0.19 (2888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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: 0.186 AC: 28256 AN: 152014 Hom.: 2879 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.186 AC: 28298 AN: 152132 Hom.: 2888 Cov.: 32 AF XY: 0.183 AC XY: 13612 AN XY: 74358

African (AFR) AF: 0.266 AC: 11029 AN: 41484

American (AMR) AF: 0.180 AC: 2756 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5180

South Asian (SAS) AF: 0.117 AC: 564 AN: 4812

European-Finnish (FIN) AF: 0.0954 AC: 1009 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10559 AN: 68000

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.173 Hom.: 1012

Bravo AF: 0.198

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs6928791; hg19: chr6-148895352;