rs1032757

chr5-82643499-G-A

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 0.15 in 152,086 control chromosomes in the GnomAD database, including 2,827 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 0.15 (2827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.150 AC: 22794 AN: 151968 Hom.: 2812 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.150 AC: 22843 AN: 152086 Hom.: 2827 Cov.: 32 AF XY: 0.148 AC XY: 10989 AN XY: 74344

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0530

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0868

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0816 Hom.: 1558

Bravo AF: 0.165

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1032757; hg19: chr5-81939318;