rs9472159

chr6-43951958-C-Achr6-43951958-C-G

Variant summary

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

The ENST00000687455.1(SCIRT):n.234-19782G>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 0.391 in 152,126 control chromosomes in the GnomAD database, including 13,432 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 0.39 (13432 hom., cov: 33)
• Consequence: SCIRT ENST00000687455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

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

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+422687C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIRT	ENST00000687455.1	n.234-19782G>T		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687158.2	n.520-19782G>T		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687843.1	n.593-19782G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59543 AN: 152008 Hom.: 13433 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.391 AC: 59536 AN: 152126 Hom.: 13432 Cov.: 33 AF XY: 0.397 AC XY: 29511 AN XY: 74366

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.389

Alfa AF: 0.468 Hom.: 29454

Bravo AF: 0.378

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9472159; hg19: chr6-43919695;