6-31264766-C-T

Variant names:

• chr6-31264766-C-T
• rs2844623

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 0.172 in 152,182 control chromosomes in the GnomAD database, including 2,290 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 (2290 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.177 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: 0.172 AC: 26174 AN: 152064 Hom.: 2288 Cov.: 34

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.172 AC: 26185 AN: 152182 Hom.: 2290 Cov.: 34 AF XY: 0.168 AC XY: 12492 AN XY: 74396

African (AFR) AF: 0.181 AC: 7491 AN: 41500

American (AMR) AF: 0.165 AC: 2519 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3472

East Asian (EAS) AF: 0.174 AC: 899 AN: 5176

South Asian (SAS) AF: 0.175 AC: 843 AN: 4830

European-Finnish (FIN) AF: 0.108 AC: 1144 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11909 AN: 68004

Other (OTH) AF: 0.184 AC: 390 AN: 2114

Alfa AF: 0.173 Hom.: 8253

Bravo AF: 0.178

Asia WGS AF: 0.154 AC: 536 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	0.49
DANN	Benign	0.76
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs2844623; hg19: chr6-31232543;