rs259598

Variant names:

• chr1-238322482-T-C
• rs259598
• ENST00000665394.1:n.194-3283T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665394.1(ENSG00000234464):​n.194-3283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 151,636 control chromosomes in the GnomAD database, including 40,103 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 0.72 (40103 hom., cov: 30)
• Consequence: ENSG00000234464 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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
ENSG00000234464	ENST00000665394.1	n.194-3283T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109764 AN: 151518 Hom.: 40074 Cov.: 30

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.724 AC: 109849 AN: 151636 Hom.: 40103 Cov.: 30 AF XY: 0.722 AC XY: 53504 AN XY: 74066

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.721

Alfa AF: 0.715 Hom.: 4837

Bravo AF: 0.735

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259598; hg19: chr1-238485782;