rs2596464

Positions:

• chr6-31445184-T-C

Variant summary

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

The NR_144465.1(LINC01149):​n.646-294T>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 0.441 in 151,596 control chromosomes in the GnomAD database, including 15,292 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 0.44 (15292 hom., cov: 32)
• Consequence: LINC01149 NR_144465.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

LINC01149 (HGNC:39757): (long intergenic non-protein coding RNA 1149)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01149	NR_144465.1	n.646-294T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01149	ENST00000430364.1	n.646-294T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66788 AN: 151478 Hom.: 15277 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.441 AC: 66843 AN: 151596 Hom.: 15292 Cov.: 32 AF XY: 0.436 AC XY: 32278 AN XY: 74110

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.473

Alfa AF: 0.484 Hom.: 18305

Bravo AF: 0.447

Asia WGS AF: 0.455 AC: 1585 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.8
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596464; hg19: chr6-31412961;