6-43799966-C-T

Position:

• chr6-43799966-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.192+2616C>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 0.514 in 151,778 control chromosomes in the GnomAD database, including 22,257 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 (22257 hom., cov: 31)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

LOC105375070 (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 (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.192+2616C>T		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+270695C>T		intron_variant			NP_001305805.1
LOC105375070	XR_007059589.1	n.192+2616C>T		intron_variant, non_coding_transcript_variant
LOC105375070	XR_926833.3	n.192+2616C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77988 AN: 151660 Hom.: 22254 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.514 AC: 78001 AN: 151778 Hom.: 22257 Cov.: 31 AF XY: 0.520 AC XY: 38571 AN XY: 74174

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.539

Alfa AF: 0.605 Hom.: 41671

Bravo AF: 0.497

Asia WGS AF: 0.613 AC: 2132 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	3.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10948095; hg19: chr6-43767703;