rs11675231

Variant names:

• chr2-226268258-A-G
• rs11675231

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 0.138 in 152,094 control chromosomes in the GnomAD database, including 1,735 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 (1735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.138 AC: 20965 AN: 151976 Hom.: 1728 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.138 AC: 20995 AN: 152094 Hom.: 1735 Cov.: 32 AF XY: 0.142 AC XY: 10565 AN XY: 74342

Gnomad4 AFR AF: 0.0803

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.136

Alfa AF: 0.147 Hom.: 1733

Bravo AF: 0.136

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11675231; hg19: chr2-227132974;