rs1032757

Variant names:

• chr5-82643499-G-A
• rs1032757

Your query was ambiguous. Multiple possible variants found:

• chr5-82643499-G-A
• chr5-82643499-G-C
• chr5-82643499-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.338 AC: 13994 AN: 41434

American (AMR) AF: 0.103 AC: 1568 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5164

South Asian (SAS) AF: 0.0868 AC: 418 AN: 4818

European-Finnish (FIN) AF: 0.0331 AC: 350 AN: 10582

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0690 AC: 4691 AN: 68000

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.0947 Hom.: 5096

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1032757; hg19: chr5-81939318;