rs11887431

Variant names:

• chr2-42040322-C-T
• rs11887431

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.278 in 152,114 control chromosomes in the GnomAD database, including 6,364 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 0.28 (6364 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.278 AC: 42311 AN: 151996 Hom.: 6360 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.278 AC: 42339 AN: 152114 Hom.: 6364 Cov.: 33 AF XY: 0.280 AC XY: 20821 AN XY: 74360

African (AFR) AF: 0.372 AC: 15432 AN: 41478

American (AMR) AF: 0.202 AC: 3085 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.0973 AC: 504 AN: 5178

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4820

European-Finnish (FIN) AF: 0.311 AC: 3285 AN: 10566

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16290 AN: 67998

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.253 Hom.: 16524

Bravo AF: 0.274

Asia WGS AF: 0.210 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.78
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs11887431; hg19: chr2-42267462;