5-132100793-G-T

Position:

• chr5-132100793-G-T

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 0.335 in 152,104 control chromosomes in the GnomAD database, including 9,672 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 0.33 (9672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50944 AN: 151986 Hom.: 9674 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.335 AC: 50943 AN: 152104 Hom.: 9672 Cov.: 32 AF XY: 0.326 AC XY: 24246 AN XY: 74366

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.364

Alfa AF: 0.425 Hom.: 23269

Bravo AF: 0.328

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10065787; hg19: chr5-131436486; COSMIC: COSV60199034;