rs2395163

Variant names:

• chr6-32420032-T-C
• rs2395163

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 0.173 in 151,950 control chromosomes in the GnomAD database, including 2,484 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 (2484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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: 0.173 AC: 26322 AN: 151830 Hom.: 2487 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.173 AC: 26318 AN: 151950 Hom.: 2484 Cov.: 31 AF XY: 0.173 AC XY: 12833 AN XY: 74278

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.163

Alfa AF: 0.201 Hom.: 4702

Bravo AF: 0.178

Asia WGS AF: 0.133 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395163; hg19: chr6-32387809;