chr5-134872338-G-T

Variant names:

• chr5-134872338-G-T
• rs10491295

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 0.0556 in 151,872 control chromosomes in the GnomAD database, including 468 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 0.056 (468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 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: 0.0555 AC: 8424 AN: 151760 Hom.: 462 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0556 AC: 8440 AN: 151872 Hom.: 468 Cov.: 32 AF XY: 0.0619 AC XY: 4593 AN XY: 74242

African (AFR) AF: 0.0129 AC: 533 AN: 41394

American (AMR) AF: 0.0753 AC: 1147 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3464

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5162

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4804

European-Finnish (FIN) AF: 0.0738 AC: 776 AN: 10522

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0493 AC: 3350 AN: 67972

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0493 Hom.: 269

Bravo AF: 0.0521

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.69
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs10491295; hg19: chr5-134208028;