rs2066432

chr6-43966925-C-T

Variant summary

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

The ENST00000687455.1(SCIRT):n.233+34118G>A 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 0.507 in 151,934 control chromosomes in the GnomAD database, including 19,984 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 0.51 (19984 hom., cov: 33)
• Consequence: SCIRT ENST00000687455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+437654C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIRT	ENST00000687455.1	n.233+34118G>A		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687158.2	n.519+32293G>A		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687843.1	n.592+32293G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77051 AN: 151816 Hom.: 19972 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.507 AC: 77094 AN: 151934 Hom.: 19984 Cov.: 33 AF XY: 0.514 AC XY: 38184 AN XY: 74278

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.525

Alfa AF: 0.496 Hom.: 4763

Bravo AF: 0.516

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066432; hg19: chr6-43934662;