6-31113428-T-C

Variant names:

• chr6-31113428-T-C
• rs2233956

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 0.119 in 152,246 control chromosomes in the GnomAD database, including 1,416 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 (1416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 49 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 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: 18050 AN: 152128 Hom.: 1416 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.119 AC: 18049 AN: 152246 Hom.: 1416 Cov.: 32 AF XY: 0.112 AC XY: 8350 AN XY: 74450

African (AFR) AF: 0.0461 AC: 1914 AN: 41552

American (AMR) AF: 0.0752 AC: 1150 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5188

South Asian (SAS) AF: 0.0775 AC: 374 AN: 4824

European-Finnish (FIN) AF: 0.0947 AC: 1004 AN: 10606

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12608 AN: 67988

Other (OTH) AF: 0.102 AC: 215 AN: 2110

Alfa AF: 0.159 Hom.: 7413

Bravo AF: 0.113

Asia WGS AF: 0.0520 AC: 183 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	5.8
DANN	Benign	0.43
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs2233956; hg19: chr6-31081205;