rs17413237

Variant names:

• chr13-103965585-T-C
• rs17413237

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0607 in 152,240 control chromosomes in the GnomAD database, including 351 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 0.061 (351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0969 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: 0.0607 AC: 9230 AN: 152122 Hom.: 349 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0607 AC: 9247 AN: 152240 Hom.: 351 Cov.: 32 AF XY: 0.0590 AC XY: 4395 AN XY: 74434

Gnomad4 AFR AF: 0.0994

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0573 Hom.: 45

Bravo AF: 0.0625

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	-0.90
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17413237; hg19: chr13-104617935;