6-43982716-T-C

Position:

• chr6-43982716-T-C

Variant summary

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

The ENST00000687455.1(SCIRT):​n.233+18327A>G 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 0.456 in 152,050 control chromosomes in the GnomAD database, including 15,905 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 0.46 (15905 hom., cov: 33)
• Consequence: SCIRT ENST00000687455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1C	NM_001318876.2	c.945+453445T>C		intron_variant			NP_001305805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCIRT	ENST00000687455.1	n.233+18327A>G		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687158.2	n.519+16502A>G		intron_variant, non_coding_transcript_variant
SCIRT	ENST00000687843.1	n.592+16502A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69234 AN: 151932 Hom.: 15900 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.456 AC: 69280 AN: 152050 Hom.: 15905 Cov.: 33 AF XY: 0.458 AC XY: 34013 AN XY: 74342

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.493

Alfa AF: 0.305 Hom.: 752

Bravo AF: 0.459

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4416670; hg19: chr6-43950453;