5-32831564-T-C

Position:

• chr5-32831564-T-C

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 0.599 in 152,010 control chromosomes in the GnomAD database, including 27,306 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 0.60 (27306 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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: 0.598 AC: 90892 AN: 151892 Hom.: 27274 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.599 AC: 90979 AN: 152010 Hom.: 27306 Cov.: 31 AF XY: 0.599 AC XY: 44468 AN XY: 74284

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.612

Alfa AF: 0.591 Hom.: 51584

Bravo AF: 0.598

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13154066; hg19: chr5-32831670;