rs4451518

Positions:

• chr1-182149187-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663078.1(LINC01344):​n.408+17899A>G 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 0.0402 in 152,290 control chromosomes in the GnomAD database, including 233 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 0.040 (233 hom., cov: 31)
• Consequence: LINC01344 ENST00000663078.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

LINC01344 (HGNC:50554): (long intergenic non-protein coding RNA 1344)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000663078.1	n.408+17899A>G		intron_variant, non_coding_transcript_variant
LINC01344	ENST00000449842.2	n.770+17899A>G		intron_variant, non_coding_transcript_variant		3
LINC01344	ENST00000608183.1	n.1913+4537A>G		intron_variant, non_coding_transcript_variant		2
LINC01344	ENST00000653755.1	n.523+17899A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6127 AN: 152170 Hom.: 233 Cov.: 31

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0402 AC: 6121 AN: 152290 Hom.: 233 Cov.: 31 AF XY: 0.0442 AC XY: 3288 AN XY: 74454

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0653

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.0403 Hom.: 22

Bravo AF: 0.0365

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4451518; hg19: chr1-182118322;