chr5-36480582-C-G

Variant names:

• chr5-36480582-C-G
• rs2468531

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 0.0513 in 152,094 control chromosomes in the GnomAD database, including 307 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 0.051 (307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7797 AN: 151976 Hom.: 302 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0513 AC: 7810 AN: 152094 Hom.: 307 Cov.: 32 AF XY: 0.0529 AC XY: 3932 AN XY: 74352

African (AFR) AF: 0.0924 AC: 3832 AN: 41474

American (AMR) AF: 0.0485 AC: 740 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5186

South Asian (SAS) AF: 0.140 AC: 673 AN: 4810

European-Finnish (FIN) AF: 0.0264 AC: 279 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0276 AC: 1879 AN: 67988

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0101 Hom.: 2

Bravo AF: 0.0514

Asia WGS AF: 0.101 AC: 348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs2468531; hg19: chr5-36480684;