rs9369425

chr6-43843237-G-Achr6-43843237-G-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+604G>A 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 0.669 in 152,058 control chromosomes in the GnomAD database, including 34,870 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 0.67 (34870 hom., cov: 32)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 (EAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.315+604G>A		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+313966G>A		intron_variant
LOC105375070	XR_007059589.1	n.315+604G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101732 AN: 151940 Hom.: 34866 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.669 AC: 101770 AN: 152058 Hom.: 34870 Cov.: 32 AF XY: 0.672 AC XY: 49965 AN XY: 74350

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.665

Alfa AF: 0.582 Hom.: 2359

Bravo AF: 0.668

Asia WGS AF: 0.775 AC: 2692 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	0.030
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369425; hg19: chr6-43810974; COSMIC: COSV56540787;