5-134501370-T-G

Variant names:

• chr5-134501370-T-G
• rs1476097

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.409 in 152,066 control chromosomes in the GnomAD database, including 13,253 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 0.41 (13253 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.409 AC: 62114 AN: 151948 Hom.: 13234 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.409 AC: 62191 AN: 152066 Hom.: 13253 Cov.: 33 AF XY: 0.416 AC XY: 30886 AN XY: 74332

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.390

Alfa AF: 0.348 Hom.: 16530

Bravo AF: 0.406

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476097; hg19: chr5-133837061;