rs55988457

chr5-97613369-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_105028.1(LINC01340):n.160-55182T>C variant causes a intron, non coding transcript 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 NR_105028.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01340	NR_105028.1	n.160-55182T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01340	ENST00000668472.1	n.160-55182T>C		intron_variant, non_coding_transcript_variant
LINC01340	ENST00000504012.1	n.160-55182T>C		intron_variant, non_coding_transcript_variant		3
LINC01340	ENST00000668863.1	n.98-55182T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.00728

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00915

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.00756

Alfa AF: 0.00985 Hom.: 2

Bravo AF: 0.00702

Asia WGS AF: 0.00115 AC: 5 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55988457; hg19: chr5-96949073;