rs17860488

chr1-159717196-CAT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.323 in 151,942 control chromosomes in the GnomAD database, including 8,502 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8502 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.323 AC: 49107 AN: 151824 Hom.: 8494 Cov.: 0

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.323 AC: 49134 AN: 151942 Hom.: 8502 Cov.: 0 AF XY: 0.327 AC XY: 24274 AN XY: 74226

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.345

Alfa AF: 0.329 Hom.: 1027

Bravo AF: 0.321

Asia WGS AF: 0.448 AC: 1557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17860488; hg19: chr1-159686986;