rs1550192

Variant names:

• chr13-112179409-T-C
• rs1550192

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 0.188 in 152,220 control chromosomes in the GnomAD database, including 3,093 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 0.19 (3093 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.188 AC: 28577 AN: 152102 Hom.: 3091 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.188 AC: 28582 AN: 152220 Hom.: 3093 Cov.: 33 AF XY: 0.198 AC XY: 14755 AN XY: 74412

African (AFR) AF: 0.115 AC: 4762 AN: 41550

American (AMR) AF: 0.216 AC: 3302 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2192 AN: 5186

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2896 AN: 10592

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12502 AN: 67992

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.195 Hom.: 1404

Bravo AF: 0.183

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.49
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs1550192; hg19: chr13-112833723;