rs1556060

Variant names:

• chr13-36135340-C-T
• rs1556060

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 0.117 in 152,208 control chromosomes in the GnomAD database, including 1,060 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 (1060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 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: 17746 AN: 152090 Hom.: 1058 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0897

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

GnomAD4 genome AF: 0.117 AC: 17757 AN: 152208 Hom.: 1060 Cov.: 32 AF XY: 0.117 AC XY: 8692 AN XY: 74406

African (AFR) AF: 0.103 AC: 4263 AN: 41538

American (AMR) AF: 0.127 AC: 1944 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5170

South Asian (SAS) AF: 0.174 AC: 841 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1067 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8068 AN: 68002

Other (OTH) AF: 0.0907 AC: 191 AN: 2106

Alfa AF: 0.118 Hom.: 1909

Bravo AF: 0.119

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.82
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1556060; hg19: chr13-36709477;