rs13170530

Variant names:

• chr5-8174075-T-C
• rs13170530

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 0.23 in 152,028 control chromosomes in the GnomAD database, including 4,198 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 0.23 (4198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.230 AC: 34908 AN: 151910 Hom.: 4194 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.230 AC: 34920 AN: 152028 Hom.: 4198 Cov.: 32 AF XY: 0.233 AC XY: 17306 AN XY: 74314

African (AFR) AF: 0.232 AC: 9622 AN: 41462

American (AMR) AF: 0.174 AC: 2650 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3470

East Asian (EAS) AF: 0.168 AC: 868 AN: 5162

South Asian (SAS) AF: 0.162 AC: 784 AN: 4828

European-Finnish (FIN) AF: 0.386 AC: 4072 AN: 10558

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15759 AN: 67976

Other (OTH) AF: 0.196 AC: 414 AN: 2114

Alfa AF: 0.221 Hom.: 16671

Bravo AF: 0.215

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.32
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs13170530; hg19: chr5-8174188;