6-43923246-G-T

Variant names:

• chr6-43923246-G-T
• rs1776721
• ENST00000691600.2:n.521-13118G>T

Variant summary

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

The NR_024478.1(LINC01512):​n.439-13118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,974 control chromosomes in the GnomAD database, including 14,453 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 0.41 (14453 hom., cov: 32)
• Consequence: LINC01512 NR_024478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 10 publications found

Genes affected

LINC01512 (HGNC:51201): (long intergenic non-protein coding RNA 1512)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024478.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01512	NR_024478.1		n.439-13118G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01512	ENST00000691600.2		n.521-13118G>T		intron	N/A
	LINC01512	ENST00000719667.1		n.241-13118G>T		intron	N/A
	LINC01512	ENST00000719668.1		n.179+12256G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61781 AN: 151856 Hom.: 14405 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.407 AC: 61882 AN: 151974 Hom.: 14453 Cov.: 32 AF XY: 0.405 AC XY: 30097 AN XY: 74272

African (AFR) AF: 0.646 AC: 26754 AN: 41442

American (AMR) AF: 0.403 AC: 6165 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 782 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1433 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3149 AN: 10526

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20777 AN: 67960

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.335 Hom.: 26106

Bravo AF: 0.423

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.20
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1776721; hg19: chr6-43890983;