rs17369571

Variant names:

• chr13-21913486-G-A
• rs17369571

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 0.196 in 152,140 control chromosomes in the GnomAD database, including 3,138 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 (3138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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: 0.196 AC: 29815 AN: 152022 Hom.: 3132 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.196 AC: 29844 AN: 152140 Hom.: 3138 Cov.: 32 AF XY: 0.192 AC XY: 14274 AN XY: 74400

African (AFR) AF: 0.262 AC: 10860 AN: 41486

American (AMR) AF: 0.133 AC: 2033 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 750 AN: 3464

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.176 AC: 847 AN: 4812

European-Finnish (FIN) AF: 0.174 AC: 1842 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12910 AN: 67982

Other (OTH) AF: 0.197 AC: 417 AN: 2116

Alfa AF: 0.189 Hom.: 6588

Bravo AF: 0.194

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.36
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs17369571; hg19: chr13-22487625;