rs4404252

Variant names:

• chr2-36672356-G-A
• rs4404252

Your query was ambiguous. Multiple possible variants found:

• chr2-36672356-G-A
• chr2-36672356-G-T

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 0.536 in 151,930 control chromosomes in the GnomAD database, including 22,088 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 0.54 (22088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.6 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: 0.536 AC: 81382 AN: 151814 Hom.: 22069 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.536 AC: 81429 AN: 151930 Hom.: 22088 Cov.: 32 AF XY: 0.538 AC XY: 40000 AN XY: 74300

African (AFR) AF: 0.454 AC: 18815 AN: 41438

American (AMR) AF: 0.606 AC: 9220 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3196 AN: 5172

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4818

European-Finnish (FIN) AF: 0.576 AC: 6094 AN: 10576

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38687 AN: 67924

Other (OTH) AF: 0.535 AC: 1126 AN: 2106

Alfa AF: 0.437 Hom.: 1332

Bravo AF: 0.538

Asia WGS AF: 0.518 AC: 1800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4404252; hg19: chr2-36899499;