rs2395162

Positions:

• chr6-32420003-G-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 0.127 in 152,064 control chromosomes in the GnomAD database, including 1,507 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 0.13 (1507 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19345 AN: 151946 Hom.: 1507 Cov.: 31

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.127 AC: 19351 AN: 152064 Hom.: 1507 Cov.: 31 AF XY: 0.124 AC XY: 9244 AN XY: 74332

Gnomad4 AFR AF: 0.0669

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.121

Alfa AF: 0.157 Hom.: 1294

Bravo AF: 0.119

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.74
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395162; hg19: chr6-32387780;