rs11895224

chr2-226058142-T-C

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 0.273 in 151,946 control chromosomes in the GnomAD database, including 6,111 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 0.27 (6111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.273 AC: 41428 AN: 151828 Hom.: 6098 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.273 AC: 41468 AN: 151946 Hom.: 6111 Cov.: 31 AF XY: 0.272 AC XY: 20227 AN XY: 74252

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.261

Alfa AF: 0.244 Hom.: 801

Bravo AF: 0.272

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
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: rs11895224; hg19: chr2-226922858;