rs17860488

Variant names:

• chr1-159717196-CAT-C
• rs17860488
• ENST00000751816.1:n.108-9330_108-9329delAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000751816.1(ENSG00000297913):​n.108-9330_108-9329delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8502 hom., cov: 0)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 1 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-9330_108-9329delAT		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-9330_110-9329delAT		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-9330_63-9329delAT		intron	N/A

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

African (AFR) AF: 0.214 AC: 8861 AN: 41484

American (AMR) AF: 0.394 AC: 6022 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3097 AN: 5140

South Asian (SAS) AF: 0.308 AC: 1470 AN: 4772

European-Finnish (FIN) AF: 0.379 AC: 3992 AN: 10530

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23244 AN: 67948

Other (OTH) AF: 0.345 AC: 727 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17860488; hg19: chr1-159686986;