rs3087271

Variant names:

• chr2-113137623-A-C
• rs3087271

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 152,164 control chromosomes in the GnomAD database, including 4,415 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 (4415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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: 34076 AN: 152046 Hom.: 4404 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0737

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.224 AC: 34104 AN: 152164 Hom.: 4415 Cov.: 32 AF XY: 0.225 AC XY: 16736 AN XY: 74392

African (AFR) AF: 0.107 AC: 4456 AN: 41534

American (AMR) AF: 0.319 AC: 4873 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3472

East Asian (EAS) AF: 0.0731 AC: 377 AN: 5160

South Asian (SAS) AF: 0.281 AC: 1353 AN: 4822

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10586

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18630 AN: 67980

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.240 Hom.: 1043

Bravo AF: 0.224

Asia WGS AF: 0.195 AC: 679 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	0.58
DANN	Benign	0.39
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs3087271; hg19: chr2-113895200;