rs1398515

Positions:

• chr17-53104552-A-G
• chr17-53104552-A-T

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 0.692 in 152,054 control chromosomes in the GnomAD database, including 41,427 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 0.69 (41427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105140 AN: 151936 Hom.: 41421 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.692 AC: 105156 AN: 152054 Hom.: 41427 Cov.: 32 AF XY: 0.697 AC XY: 51786 AN XY: 74322

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.744

Alfa AF: 0.789 Hom.: 8349

Bravo AF: 0.668

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398515; hg19: chr17-51181913;