ENST00000715761.1:n.277+25589T>C

Variant names:

• chr5-97696273-T-C
• rs6867755
• ENST00000715761.1:n.277+25589T>C

Variant summary

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

The ENST00000715761.1(LINC01340):​n.277+25589T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,186 control chromosomes in the GnomAD database, including 445 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 0.049 (445 hom., cov: 32)
• Consequence: LINC01340 ENST00000715761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 0 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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715761.1. 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
	LINC01340	ENST00000715761.1		n.277+25589T>C		intron	N/A
	LINC01340	ENST00000746238.1		n.382+25589T>C		intron	N/A
	LINC01340	ENST00000746239.1		n.362+25589T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7430 AN: 152068 Hom.: 440 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00390

Gnomad OTH AF: 0.0439

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

GnomAD4 genome AF: 0.0491 AC: 7465 AN: 152186 Hom.: 445 Cov.: 32 AF XY: 0.0496 AC XY: 3692 AN XY: 74404

African (AFR) AF: 0.135 AC: 5609 AN: 41530

American (AMR) AF: 0.0370 AC: 565 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3468

East Asian (EAS) AF: 0.0900 AC: 465 AN: 5166

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4820

European-Finnish (FIN) AF: 0.0316 AC: 335 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00390 AC: 265 AN: 68012

Other (OTH) AF: 0.0458 AC: 97 AN: 2116

Alfa AF: 0.0174 Hom.: 133

Bravo AF: 0.0546

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	10
DANN	Benign	0.42
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6867755; hg19: chr5-97031977;