5-101522490-C-T

Variant names:

• chr5-101522490-C-T
• rs10515310

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 0.0661 in 151,712 control chromosomes in the GnomAD database, including 925 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 0.066 (925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10003 AN: 151592 Hom.: 921 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00540

Gnomad FIN AF: 0.000380

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.00913

Gnomad OTH AF: 0.0625

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

GnomAD4 genome AF: 0.0661 AC: 10034 AN: 151712 Hom.: 925 Cov.: 32 AF XY: 0.0645 AC XY: 4778 AN XY: 74118

African (AFR) AF: 0.207 AC: 8583 AN: 41380

American (AMR) AF: 0.0341 AC: 519 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00520 AC: 25 AN: 4808

European-Finnish (FIN) AF: 0.000380 AC: 4 AN: 10538

Middle Eastern (MID) AF: 0.0483 AC: 14 AN: 290

European-Non Finnish (NFE) AF: 0.00913 AC: 619 AN: 67818

Other (OTH) AF: 0.0618 AC: 130 AN: 2104

Alfa AF: 0.00375 Hom.: 3

Bravo AF: 0.0768

Asia WGS AF: 0.0130 AC: 45 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.46
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10515310; hg19: chr5-100858194;