rs17368525

Positions:

• chr13-21893850-G-A
• chr13-21893850-G-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 0.459 in 151,820 control chromosomes in the GnomAD database, including 16,413 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 0.46 (16413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 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: 0.459 AC: 69583 AN: 151702 Hom.: 16392 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.459 AC: 69649 AN: 151820 Hom.: 16413 Cov.: 31 AF XY: 0.463 AC XY: 34324 AN XY: 74158

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.482

Alfa AF: 0.478 Hom.: 21912

Bravo AF: 0.458

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17368525; hg19: chr13-22467989;