rs1429862

Variant names:

• chr5-97737115-C-T
• rs1429862
• ENST00000715761.1:n.277+66431C>T

Variant summary

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

The ENST00000715761.1(LINC01340):​n.277+66431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,756 control chromosomes in the GnomAD database, including 1,260 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 0.11 (1260 hom., cov: 32)
• Consequence: LINC01340 ENST00000715761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 2 publications found

Genes affected

LINC01340 (HGNC:50550): (long intergenic non-protein coding RNA 1340)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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
LINC01340	ENST00000715761.1	n.277+66431C>T		intron_variant	Intron 3 of 6
LINC01340	ENST00000746238.1	n.382+66431C>T		intron_variant	Intron 4 of 8
LINC01340	ENST00000746239.1	n.362+66431C>T		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16712 AN: 151638 Hom.: 1259 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.110 AC: 16727 AN: 151756 Hom.: 1260 Cov.: 32 AF XY: 0.111 AC XY: 8213 AN XY: 74158

African (AFR) AF: 0.115 AC: 4784 AN: 41468

American (AMR) AF: 0.109 AC: 1657 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3466

East Asian (EAS) AF: 0.174 AC: 902 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1085 AN: 4808

European-Finnish (FIN) AF: 0.0661 AC: 694 AN: 10506

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6745 AN: 67776

Other (OTH) AF: 0.118 AC: 249 AN: 2102

Alfa AF: 0.113 Hom.: 711

Bravo AF: 0.108

Asia WGS AF: 0.213 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.31
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1429862; hg19: chr5-97072819;