rs11894842

chr2-200908822-T-Cchr2-200908822-T-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 0.316 in 151,722 control chromosomes in the GnomAD database, including 10,002 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 0.32 (10002 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.316 AC: 47848 AN: 151602 Hom.: 9976 Cov.: 30

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.316 AC: 47932 AN: 151722 Hom.: 10002 Cov.: 30 AF XY: 0.311 AC XY: 23030 AN XY: 74120

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.291

Alfa AF: 0.240 Hom.: 5336

Bravo AF: 0.327

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11894842; hg19: chr2-201773545;