rs17523405

Variant names:

• chr13-27305470-T-C
• rs17523405

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 0.087 in 150,096 control chromosomes in the GnomAD database, including 841 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 0.087 (841 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0871 AC: 13058 AN: 149980 Hom.: 841 Cov.: 29

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0872

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0870 AC: 13055 AN: 150096 Hom.: 841 Cov.: 29 AF XY: 0.0891 AC XY: 6518 AN XY: 73124

African (AFR) AF: 0.0176 AC: 724 AN: 41064

American (AMR) AF: 0.0726 AC: 1084 AN: 14938

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 296 AN: 3460

East Asian (EAS) AF: 0.00118 AC: 6 AN: 5100

South Asian (SAS) AF: 0.0309 AC: 148 AN: 4782

European-Finnish (FIN) AF: 0.220 AC: 2154 AN: 9784

Middle Eastern (MID) AF: 0.117 AC: 34 AN: 290

European-Non Finnish (NFE) AF: 0.124 AC: 8364 AN: 67688

Other (OTH) AF: 0.0797 AC: 166 AN: 2084

Alfa AF: 0.115 Hom.: 899

Bravo AF: 0.0733

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs17523405; hg19: chr13-27879607;