chr5-131127653-C-T

Position:

• chr5-131127653-C-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 0.0881 in 151,798 control chromosomes in the GnomAD database, including 791 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 0.088 (791 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13381 AN: 151678 Hom.: 789 Cov.: 31

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0881 AC: 13380 AN: 151798 Hom.: 791 Cov.: 31 AF XY: 0.0906 AC XY: 6718 AN XY: 74156

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0410

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0857

Alfa AF: 0.0467 Hom.: 50

Bravo AF: 0.0765

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12517633; hg19: chr5-130463346;