6-31193433-T-G

Variant names:

• chr6-31193433-T-G
• rs3095238

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 0.876 in 151,716 control chromosomes in the GnomAD database, including 58,272 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 0.88 (58272 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.876 AC: 132757 AN: 151598 Hom.: 58222 Cov.: 28

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.876 AC: 132862 AN: 151716 Hom.: 58272 Cov.: 28 AF XY: 0.876 AC XY: 64923 AN XY: 74098

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.905

Alfa AF: 0.862 Hom.: 18762

Bravo AF: 0.880

Asia WGS AF: 0.833 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095238; hg19: chr6-31161210;