rs1556459

Variant names:

• chr10-129012447-T-C
• rs1556459

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 0.201 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.345 AC: 14251 AN: 41344

American (AMR) AF: 0.178 AC: 2710 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3462

East Asian (EAS) AF: 0.189 AC: 973 AN: 5152

South Asian (SAS) AF: 0.154 AC: 740 AN: 4808

European-Finnish (FIN) AF: 0.145 AC: 1528 AN: 10526

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9351 AN: 67814

Other (OTH) AF: 0.160 AC: 335 AN: 2096

Alfa AF: 0.197 Hom.: 701

Bravo AF: 0.211

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.86
DANN	Benign	0.37
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1556459; hg19: chr10-130810711;