5-130589629-T-C

Variant names:

• chr5-130589629-T-C
• rs2215257

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 0.469 in 151,896 control chromosomes in the GnomAD database, including 17,531 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 0.47 (17531 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.469 AC: 71218 AN: 151778 Hom.: 17495 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.469 AC: 71314 AN: 151896 Hom.: 17531 Cov.: 31 AF XY: 0.477 AC XY: 35386 AN XY: 74240

African (AFR) AF: 0.588 AC: 24372 AN: 41414

American (AMR) AF: 0.465 AC: 7099 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3187 AN: 5134

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4816

European-Finnish (FIN) AF: 0.523 AC: 5519 AN: 10556

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26001 AN: 67916

Other (OTH) AF: 0.429 AC: 903 AN: 2104

Alfa AF: 0.403 Hom.: 21173

Bravo AF: 0.467

Asia WGS AF: 0.581 AC: 2021 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	4.8
DANN	Benign	0.75
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2215257; hg19: chr5-129925322;