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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.172 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

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.183

Alfa AF: 0.178 Hom.: 318

Bravo AF: 0.165

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs392162; hg19: chr7-137999654;