rs2233969

chr6-31112655-A-G

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 0.188 in 762,804 control chromosomes in the GnomAD database, including 15,157 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 0.16 (2236 hom., cov: 33)
  • Exomes 𝑓: 0.20 (12921 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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: 0.160 AC: 24414 AN: 152134 Hom.: 2239 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.195 AC: 119182 AN: 610552 Hom.: 12921 AF XY: 0.199 AC XY: 61989 AN XY: 311206

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.289

Gnomad4 FIN exome AF: 0.140

Gnomad4 NFE exome AF: 0.183

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.160 AC: 24423 AN: 152252 Hom.: 2236 Cov.: 33 AF XY: 0.162 AC XY: 12026 AN XY: 74442

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.160

Alfa AF: 0.160 Hom.: 188

Bravo AF: 0.156

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	11
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233969; hg19: chr6-31080432;