rs1562432

Variant names:

• chr8-127495357-T-C
• rs1562432

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 0.117 in 152,186 control chromosomes in the GnomAD database, including 1,265 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 0.12 (1265 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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: 0.117 AC: 17858 AN: 152068 Hom.: 1266 Cov.: 31

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.117 AC: 17858 AN: 152186 Hom.: 1265 Cov.: 31 AF XY: 0.117 AC XY: 8732 AN XY: 74378

Gnomad4 AFR AF: 0.0489

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.114

Alfa AF: 0.135 Hom.: 1634

Bravo AF: 0.111

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.018
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562432; hg19: chr8-128507602;