rs17425287

Variant names:

• chr1-79820726-T-C
• rs17425287

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 0.509 in 151,762 control chromosomes in the GnomAD database, including 20,188 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 0.51 (20188 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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: 0.509 AC: 77185 AN: 151644 Hom.: 20179 Cov.: 30

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.509 AC: 77228 AN: 151762 Hom.: 20188 Cov.: 30 AF XY: 0.513 AC XY: 38029 AN XY: 74146

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.514

Alfa AF: 0.543 Hom.: 29865

Bravo AF: 0.502

Asia WGS AF: 0.417 AC: 1447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17425287; hg19: chr1-80286411; COSMIC: COSV59960591;