rs2233967

Variant names:

• chr6-31113051-C-G
• rs2233967

Your query was ambiguous. Multiple possible variants found:

• chr6-31113051-C-G
• chr6-31113051-C-T

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 0.14 in 152,196 control chromosomes in the GnomAD database, including 1,761 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 (1761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.140 AC: 21273 AN: 152078 Hom.: 1764 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.140 AC: 21280 AN: 152196 Hom.: 1761 Cov.: 32 AF XY: 0.141 AC XY: 10495 AN XY: 74402

African (AFR) AF: 0.0699 AC: 2903 AN: 41542

American (AMR) AF: 0.152 AC: 2331 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5170

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1436 AN: 10598

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

European-Non Finnish (NFE) AF: 0.161 AC: 10983 AN: 68008

Other (OTH) AF: 0.146 AC: 307 AN: 2106

Alfa AF: 0.148 Hom.: 1025

Bravo AF: 0.134

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.55
PhyloP100		-2.3
PromoterAI		-0.0030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2233967; hg19: chr6-31080828;