rs2036524

Variant names:

• chr2-163205924-C-T
• rs2036524

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.898 in 151,980 control chromosomes in the GnomAD database, including 61,523 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 0.90 (61523 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.898 AC: 136420 AN: 151862 Hom.: 61511 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.898 AC: 136478 AN: 151980 Hom.: 61523 Cov.: 30 AF XY: 0.895 AC XY: 66506 AN XY: 74268

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.894

Alfa AF: 0.919 Hom.: 8006

Bravo AF: 0.892

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036524; hg19: chr2-164062434;