rs4394275

Variant names:

• chr6-31350400-G-A
• rs4394275

Your query was ambiguous. Multiple possible variants found:

• chr6-31350400-G-A
• chr6-31350400-G-C

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 0.265 in 152,090 control chromosomes in the GnomAD database, including 5,481 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 0.26 (5481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

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 (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.265 AC: 40241 AN: 151972 Hom.: 5480 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.265 AC: 40275 AN: 152090 Hom.: 5481 Cov.: 32 AF XY: 0.268 AC XY: 19906 AN XY: 74348

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.246

Alfa AF: 0.239 Hom.: 6239

Bravo AF: 0.258

Asia WGS AF: 0.215 AC: 749 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	9.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4394275; hg19: chr6-31318177;