chr6-43929990-C-T

Position:

• chr6-43929990-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_024478.1(LINC01512):​n.439-6374C>T 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 0.276 in 152,062 control chromosomes in the GnomAD database, including 6,169 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 0.28 (6169 hom., cov: 32)
• Consequence: LINC01512 NR_024478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

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

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01512	NR_024478.1	n.439-6374C>T		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+400719C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01512	ENST00000691600.1	n.422-6374C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41845 AN: 151944 Hom.: 6155 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.276 AC: 41895 AN: 152062 Hom.: 6169 Cov.: 32 AF XY: 0.278 AC XY: 20677 AN XY: 74322

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.236

Alfa AF: 0.226 Hom.: 9235

Bravo AF: 0.278

Asia WGS AF: 0.227 AC: 791 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9472155; hg19: chr6-43897727;