chr2-15817284-T-C

Variant names:

• chr2-15817284-T-C
• rs4669002

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 0.732 in 152,206 control chromosomes in the GnomAD database, including 43,336 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 0.73 (43336 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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: 0.732 AC: 111319 AN: 152088 Hom.: 43322 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.732 AC: 111383 AN: 152206 Hom.: 43336 Cov.: 33 AF XY: 0.735 AC XY: 54704 AN XY: 74422

African (AFR) AF: 0.443 AC: 18371 AN: 41496

American (AMR) AF: 0.812 AC: 12416 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3764 AN: 5170

South Asian (SAS) AF: 0.799 AC: 3851 AN: 4820

European-Finnish (FIN) AF: 0.850 AC: 9012 AN: 10602

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58367 AN: 68030

Other (OTH) AF: 0.763 AC: 1615 AN: 2116

Alfa AF: 0.791 Hom.: 6138

Bravo AF: 0.713

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.71
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4669002; hg19: chr2-15957408;