rs1558103

Variant names:

• chr17-12291963-T-A
• rs1558103

Your query was ambiguous. Multiple possible variants found:

• chr17-12291963-T-A
• chr17-12291963-T-C
• chr17-12291963-T-G

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 0.914 in 152,226 control chromosomes in the GnomAD database, including 64,748 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 0.91 (64748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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: 0.915 AC: 139109 AN: 152110 Hom.: 64729 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.914 AC: 139177 AN: 152226 Hom.: 64748 Cov.: 32 AF XY: 0.917 AC XY: 68227 AN XY: 74432

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.927

Alfa AF: 0.948 Hom.: 8588

Bravo AF: 0.902

Asia WGS AF: 0.966 AC: 3361 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	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558103; hg19: chr17-12195280;