7-138313605-G-A

Variant names:

• chr7-138313605-G-A
• rs402358

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 0.171 in 152,106 control chromosomes in the GnomAD database, including 2,685 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 0.17 (2685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26005 AN: 151988 Hom.: 2687 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.171 AC: 25994 AN: 152106 Hom.: 2685 Cov.: 32 AF XY: 0.174 AC XY: 12929 AN XY: 74356

African (AFR) AF: 0.0724 AC: 3006 AN: 41526

American (AMR) AF: 0.182 AC: 2783 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 671 AN: 3464

East Asian (EAS) AF: 0.309 AC: 1591 AN: 5144

South Asian (SAS) AF: 0.366 AC: 1757 AN: 4804

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10584

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13976 AN: 67998

Other (OTH) AF: 0.180 AC: 380 AN: 2106

Alfa AF: 0.177 Hom.: 315

Bravo AF: 0.165

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.17
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs402358; hg19: chr7-137998350;