rs2395174

Variant names:

• chr6-32437101-T-G
• rs2395174

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 0.238 in 152,122 control chromosomes in the GnomAD database, including 4,871 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 0.24 (4871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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: 0.238 AC: 36219 AN: 152004 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.238 AC: 36242 AN: 152122 Hom.: 4871 Cov.: 31 AF XY: 0.241 AC XY: 17896 AN XY: 74348

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.234

Alfa AF: 0.260 Hom.: 2823

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.30
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395174; hg19: chr6-32404878;