chr6-43762907-A-T

Position:

• chr6-43762907-A-T

Variant summary

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

The NM_001318876.2(POLR1C):​c.945+233636A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,194 control chromosomes in the GnomAD database, including 1,685 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 0.15 (1685 hom., cov: 32)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1C	NM_001318876.2	c.945+233636A>T		intron_variant			NP_001305805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22758 AN: 152074 Hom.: 1685 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.150 AC: 22772 AN: 152194 Hom.: 1685 Cov.: 32 AF XY: 0.152 AC XY: 11305 AN XY: 74428

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0929 Hom.: 121

Bravo AF: 0.140

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
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: rs1547651; hg19: chr6-43730644;