rs11902417

chr2-20976028-G-Achr2-20976028-G-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 0.255 in 152,098 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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 = 0.705 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: 0.255 AC: 38797 AN: 151980 Hom.: 5844 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.255 AC: 38804 AN: 152098 Hom.: 5842 Cov.: 33 AF XY: 0.262 AC XY: 19445 AN XY: 74336

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.255

Alfa AF: 0.264 Hom.: 7610

Bravo AF: 0.249

Asia WGS AF: 0.587 AC: 2039 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	2.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11902417; hg19: chr2-21198900;