7-109161567-G-T

Variant names:

• chr7-109161567-G-T
• rs6951925

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 0.779 in 149,836 control chromosomes in the GnomAD database, including 46,393 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 0.78 (46393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.779 AC: 116707 AN: 149730 Hom.: 46357 Cov.: 30

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.779 AC: 116794 AN: 149836 Hom.: 46393 Cov.: 30 AF XY: 0.766 AC XY: 55942 AN XY: 73048

African (AFR) AF: 0.863 AC: 35576 AN: 41218

American (AMR) AF: 0.757 AC: 11393 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3136 AN: 3446

East Asian (EAS) AF: 0.214 AC: 1069 AN: 4998

South Asian (SAS) AF: 0.646 AC: 3074 AN: 4758

European-Finnish (FIN) AF: 0.656 AC: 6610 AN: 10082

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53178 AN: 67008

Other (OTH) AF: 0.808 AC: 1677 AN: 2076

Alfa AF: 0.780 Hom.: 71719

Bravo AF: 0.788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.36
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs6951925; hg19: chr7-108801624;