rs392162

Variant names:

• chr7-138314909-A-G
• rs392162

Your query was ambiguous. Multiple possible variants found:

• chr7-138314909-A-G
• chr7-138314909-A-T

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 0.172 in 152,062 control chromosomes in the GnomAD database, including 2,709 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 (2709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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: 0.172 AC: 26154 AN: 151946 Hom.: 2712 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.172 AC: 26142 AN: 152062 Hom.: 2709 Cov.: 32 AF XY: 0.175 AC XY: 13008 AN XY: 74322

African (AFR) AF: 0.0730 AC: 3029 AN: 41514

American (AMR) AF: 0.182 AC: 2780 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1601 AN: 5168

South Asian (SAS) AF: 0.369 AC: 1774 AN: 4810

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10576

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13993 AN: 67958

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.174 Hom.: 320

Bravo AF: 0.165

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.31
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs392162; hg19: chr7-137999654; COSMIC: COSV107155592;