chr5-36454029-C-T

Variant names:

• chr5-36454029-C-T
• rs2468513

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 0.0922 in 149,766 control chromosomes in the GnomAD database, including 787 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 0.092 (787 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.159 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: 0.0921 AC: 13781 AN: 149648 Hom.: 783 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0199

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0922 AC: 13804 AN: 149766 Hom.: 787 Cov.: 33 AF XY: 0.0930 AC XY: 6789 AN XY: 72978

African (AFR) AF: 0.159 AC: 6568 AN: 41256

American (AMR) AF: 0.0724 AC: 1071 AN: 14792

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 206 AN: 3424

East Asian (EAS) AF: 0.0376 AC: 193 AN: 5132

South Asian (SAS) AF: 0.169 AC: 781 AN: 4622

European-Finnish (FIN) AF: 0.0552 AC: 544 AN: 9856

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0625 AC: 4215 AN: 67430

Other (OTH) AF: 0.0904 AC: 186 AN: 2058

Alfa AF: 0.0780 Hom.: 83

Bravo AF: 0.0898

Asia WGS AF: 0.116 AC: 402 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2468513; hg19: chr5-36454131;