chr7-117973233-G-A

Variant names:

• chr7-117973233-G-A
• rs12706164

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 0.149 in 151,194 control chromosomes in the GnomAD database, including 1,939 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 0.15 (1939 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22585 AN: 151090 Hom.: 1942 Cov.: 31

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.149 AC: 22572 AN: 151194 Hom.: 1939 Cov.: 31 AF XY: 0.144 AC XY: 10600 AN XY: 73802

African (AFR) AF: 0.0614 AC: 2526 AN: 41164

American (AMR) AF: 0.151 AC: 2291 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3462

East Asian (EAS) AF: 0.116 AC: 594 AN: 5128

South Asian (SAS) AF: 0.0843 AC: 403 AN: 4782

European-Finnish (FIN) AF: 0.161 AC: 1664 AN: 10308

Middle Eastern (MID) AF: 0.190 AC: 55 AN: 290

European-Non Finnish (NFE) AF: 0.205 AC: 13916 AN: 67868

Other (OTH) AF: 0.174 AC: 365 AN: 2098

Alfa AF: 0.190 Hom.: 5314

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.3
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12706164; hg19: chr7-117613287;