rs11884632

Variant names:

• chr2-189560116-G-C
• rs11884632

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 0.224 in 152,068 control chromosomes in the GnomAD database, including 4,063 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 0.22 (4063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 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: 0.224 AC: 34072 AN: 151950 Hom.: 4059 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.224 AC: 34090 AN: 152068 Hom.: 4063 Cov.: 32 AF XY: 0.224 AC XY: 16626 AN XY: 74312

African (AFR) AF: 0.182 AC: 7555 AN: 41484

American (AMR) AF: 0.165 AC: 2527 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3472

East Asian (EAS) AF: 0.113 AC: 583 AN: 5156

South Asian (SAS) AF: 0.168 AC: 810 AN: 4818

European-Finnish (FIN) AF: 0.323 AC: 3407 AN: 10552

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17930 AN: 67984

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.246 Hom.: 647

Bravo AF: 0.209

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.6
DANN	Benign	0.84
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11884632; hg19: chr2-190424842;