rs2394895

Variant names:

• chr6-31239202-T-C
• rs2394895

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,194 control chromosomes in the GnomAD database, including 3,449 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 0.21 (3449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 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: 0.209 AC: 31741 AN: 152076 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.209 AC: 31746 AN: 152194 Hom.: 3449 Cov.: 32 AF XY: 0.203 AC XY: 15081 AN XY: 74432

African (AFR) AF: 0.161 AC: 6699 AN: 41544

American (AMR) AF: 0.177 AC: 2708 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5176

South Asian (SAS) AF: 0.144 AC: 694 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1749 AN: 10598

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17014 AN: 67974

Other (OTH) AF: 0.216 AC: 456 AN: 2114

Alfa AF: 0.235 Hom.: 14338

Bravo AF: 0.208

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.6
DANN	Benign	0.89
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2394895; hg19: chr6-31206979;