rs2596464

Variant names:

• chr6-31445184-T-C
• rs2596464
• ENST00000430364.1:n.646-294T>C

Variant summary

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

The ENST00000430364.1(LINC01149):​n.646-294T>C variant causes a intron 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 ENST00000430364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 35 publications found

Genes affected

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

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01149	NR_144465.1	n.646-294T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01149	ENST00000430364.1	n.646-294T>C		intron_variant	Intron 1 of 1	1
ENSG00000288587	ENST00000673857.1	n.63-17939T>C		intron_variant	Intron 1 of 2
LINC01149	ENST00000812003.1	n.669+2873T>C		intron_variant	Intron 1 of 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

African (AFR) AF: 0.346 AC: 14246 AN: 41180

American (AMR) AF: 0.468 AC: 7086 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1721 AN: 3464

East Asian (EAS) AF: 0.488 AC: 2514 AN: 5152

South Asian (SAS) AF: 0.440 AC: 2117 AN: 4808

European-Finnish (FIN) AF: 0.369 AC: 3900 AN: 10562

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33772 AN: 67970

Other (OTH) AF: 0.473 AC: 993 AN: 2100

Alfa AF: 0.482 Hom.: 34328

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2596464; hg19: chr6-31412961;