chr6-43860845-T-C

Position:

• chr6-43860845-T-C

Variant summary

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

The XR_007059588.1(LOC105375070):​n.315+18212T>C 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 0.371 in 152,186 control chromosomes in the GnomAD database, including 12,445 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 0.37 (12445 hom., cov: 34)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

LOC105375070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.315+18212T>C		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+331574T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56467 AN: 152068 Hom.: 12446 Cov.: 34

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.371 AC: 56469 AN: 152186 Hom.: 12445 Cov.: 34 AF XY: 0.366 AC XY: 27240 AN XY: 74410

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.382

Alfa AF: 0.465 Hom.: 16980

Bravo AF: 0.365

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711751; hg19: chr6-43828582;