rs9472138

chr6-43844025-C-T

Variant summary

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

The XR_007059588.1(LOC105375070):n.315+1392C>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 0.244 in 152,154 control chromosomes in the GnomAD database, including 4,787 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 0.24 (4787 hom., cov: 32)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LOC105375070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.315+1392C>T		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+314754C>T		intron_variant
LOC105375070	XR_007059589.1	n.316-1251C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37071 AN: 152038 Hom.: 4784 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.244 AC: 37097 AN: 152154 Hom.: 4787 Cov.: 32 AF XY: 0.243 AC XY: 18103 AN XY: 74380

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.267

Alfa AF: 0.273 Hom.: 13753

Bravo AF: 0.234

Asia WGS AF: 0.182 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9472138; hg19: chr6-43811762;