rs1556459

chr10-129012447-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 0.201 in 151,598 control chromosomes in the GnomAD database, including 3,624 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 0.20 (3624 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.201 AC: 30372 AN: 151480 Hom.: 3609 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.201 AC: 30424 AN: 151598 Hom.: 3624 Cov.: 33 AF XY: 0.200 AC XY: 14812 AN XY: 74098

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.160

Alfa AF: 0.193 Hom.: 663

Bravo AF: 0.211

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.86
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556459; hg19: chr10-130810711;