6-31113122-T-G

Variant names:

• chr6-31113122-T-G
• rs2233965

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 0.143 in 152,158 control chromosomes in the GnomAD database, including 1,785 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 0.14 (1785 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21772 AN: 152040 Hom.: 1788 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.143 AC: 21779 AN: 152158 Hom.: 1785 Cov.: 32 AF XY: 0.144 AC XY: 10704 AN XY: 74376

African (AFR) AF: 0.0821 AC: 3411 AN: 41522

American (AMR) AF: 0.153 AC: 2339 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1529 AN: 5164

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4814

European-Finnish (FIN) AF: 0.134 AC: 1422 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10987 AN: 67996

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.157 Hom.: 6915

Bravo AF: 0.138

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2233965; hg19: chr6-31080899;