rs2233967

chr6-31113051-C-Gchr6-31113051-C-T

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 0.14 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0437 Hom.: 41

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233967; hg19: chr6-31080828;