rs1923254

Variant names:

• chr13-40510104-A-G
• rs1923254
• ENST00000615137.1:n.142+25562T>C

Variant summary

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

The ENST00000615137.1(LINC00598):​n.142+25562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,812 control chromosomes in the GnomAD database, including 35,200 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 0.66 (35200 hom., cov: 31)
• Consequence: LINC00598 ENST00000615137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ENSG00000288542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 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
LINC00598	ENST00000615137.1	n.142+25562T>C		intron_variant	Intron 1 of 3	3
ENSG00000288542	ENST00000636651.2	n.1460-36009T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100181 AN: 151696 Hom.: 35196 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.660 AC: 100195 AN: 151812 Hom.: 35200 Cov.: 31 AF XY: 0.659 AC XY: 48932 AN XY: 74210

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.647

Alfa AF: 0.751 Hom.: 79668

Bravo AF: 0.645

Asia WGS AF: 0.420 AC: 1461 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.2
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923254; hg19: chr13-41084241;