rs2395173

Variant names:

• chr6-32437082-A-G
• rs2395173

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 0.625 in 152,090 control chromosomes in the GnomAD database, including 30,289 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 0.63 (30289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.625 AC: 95041 AN: 151972 Hom.: 30286 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.625 AC: 95085 AN: 152090 Hom.: 30289 Cov.: 31 AF XY: 0.630 AC XY: 46846 AN XY: 74340

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.647

Alfa AF: 0.676 Hom.: 19357

Bravo AF: 0.615

Asia WGS AF: 0.675 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395173; hg19: chr6-32404859;