rs2395175

Variant names:

• chr6-32437249-G-A
• rs2395175

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 0.119 in 152,178 control chromosomes in the GnomAD database, including 1,294 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 0.12 (1294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

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 = 0.156 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: 0.119 AC: 18086 AN: 152060 Hom.: 1295 Cov.: 31

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.119 AC: 18094 AN: 152178 Hom.: 1294 Cov.: 31 AF XY: 0.116 AC XY: 8632 AN XY: 74396

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0672

Gnomad4 SAS AF: 0.0808

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.144 Hom.: 2220

Bravo AF: 0.120

Asia WGS AF: 0.0680 AC: 240 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	8.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395175; hg19: chr6-32405026; COSMIC: COSV66622731;