rs17413237

chr13-103965585-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;