rs844294

chr6-43932970-T-Cchr6-43932970-T-G

Variant summary

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

The NR_024478.1(LINC01512):n.439-3394T>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 0.555 in 151,950 control chromosomes in the GnomAD database, including 24,292 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 0.55 (24292 hom., cov: 31)
• Consequence: LINC01512 NR_024478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

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

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01512	NR_024478.1	n.439-3394T>C		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+403699T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIRT	ENST00000687455.1	n.234-794A>G		intron_variant, non_coding_transcript_variant
LINC01512	ENST00000691600.1	n.422-3394T>C		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687158.2	n.520-794A>G		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687843.1	n.593-794A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84193 AN: 151832 Hom.: 24248 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.555 AC: 84283 AN: 151950 Hom.: 24292 Cov.: 31 AF XY: 0.550 AC XY: 40878 AN XY: 74270

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.566

Alfa AF: 0.512 Hom.: 19066

Bravo AF: 0.574

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.028
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844294; hg19: chr6-43900707;