rs6923866

chr6-43933447-T-C

Variant summary

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

The NR_024478.1(LINC01512):n.439-2917T>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 0.295 in 152,114 control chromosomes in the GnomAD database, including 7,165 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 0.30 (7165 hom., cov: 32)
• Consequence: LINC01512 NR_024478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01512	NR_024478.1	n.439-2917T>C		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+404176T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIRT	ENST00000687455.1	n.234-1271A>G		intron_variant, non_coding_transcript_variant
LINC01512	ENST00000691600.1	n.422-2917T>C		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687158.2	n.520-1271A>G		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687843.1	n.593-1271A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44873 AN: 151996 Hom.: 7135 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.295 AC: 44949 AN: 152114 Hom.: 7165 Cov.: 32 AF XY: 0.290 AC XY: 21541 AN XY: 74368

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.325

Alfa AF: 0.269 Hom.: 1761

Bravo AF: 0.312

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	16
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6923866; hg19: chr6-43901184;