rs55988457

Variant names:

• chr5-97613369-T-C
• rs55988457
• ENST00000504012.2:n.160-55182T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000504012.2(LINC01340):​n.160-55182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00748 in 152,188 control chromosomes in the GnomAD database, including 9 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 0.0075 (9 hom., cov: 32)
• Consequence: LINC01340 ENST00000504012.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd4 at 9 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504012.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01340	NR_105028.1		n.160-55182T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01340	ENST00000504012.2	TSL:3	n.160-55182T>C		intron	N/A
	LINC01340	ENST00000668472.1		n.160-55182T>C		intron	N/A
	LINC01340	ENST00000668863.2		n.205-55182T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00749 AC: 1139 AN: 152070 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00729

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00915

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.00764

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

GnomAD4 genome AF: 0.00748 AC: 1138 AN: 152188 Hom.: 9 Cov.: 32 AF XY: 0.00739 AC XY: 550 AN XY: 74410

African (AFR) AF: 0.00226 AC: 94 AN: 41548

American (AMR) AF: 0.00728 AC: 111 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.00915 AC: 97 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 757 AN: 67992

Other (OTH) AF: 0.00756 AC: 16 AN: 2116

Alfa AF: 0.00931 Hom.: 4

Bravo AF: 0.00702

Asia WGS AF: 0.00115 AC: 5 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.54
PhyloP100		1.8
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: rs55988457; hg19: chr5-96949073;