rs17025426

Variant names:

• chr1-110102705-C-T
• rs17025426
• ENST00000554808.1:n.166-6140C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554808.1(LINC01397):​n.166-6140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,186 control chromosomes in the GnomAD database, including 1,234 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 0.10 (1234 hom., cov: 32)
• Consequence: LINC01397 ENST00000554808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 7 publications found

Genes affected

LINC01397 (HGNC:50677): (long intergenic non-protein coding RNA 1397)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01397	NR_126382.1	n.166-6140C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01397	ENST00000554808.1	n.166-6140C>T		intron_variant	Intron 1 of 3	4
LINC01397	ENST00000751945.1	n.166-6140C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15239 AN: 152068 Hom.: 1230 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.100 AC: 15277 AN: 152186 Hom.: 1234 Cov.: 32 AF XY: 0.0987 AC XY: 7346 AN XY: 74406

African (AFR) AF: 0.218 AC: 9040 AN: 41474

American (AMR) AF: 0.0531 AC: 813 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.0795 AC: 384 AN: 4830

European-Finnish (FIN) AF: 0.0640 AC: 679 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3893 AN: 68008

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0720 Hom.: 2126

Bravo AF: 0.105

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17025426; hg19: chr1-110645327;