6-43836834-T-G

Position:

• chr6-43836834-T-G

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-5677T>G 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 0.782 in 151,814 control chromosomes in the GnomAD database, including 46,867 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 0.78 (46867 hom., cov: 28)
• Consequence: ENST00000637813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.193-5677T>G		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+307563T>G		intron_variant			NP_001305805.1
LOC105375070	XR_007059589.1	n.193-5677T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000637813.1	n.366-5677T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118662 AN: 151696 Hom.: 46823 Cov.: 28

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.782 AC: 118766 AN: 151814 Hom.: 46867 Cov.: 28 AF XY: 0.784 AC XY: 58148 AN XY: 74188

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.769

Alfa AF: 0.743 Hom.: 11671

Bravo AF: 0.794

Asia WGS AF: 0.822 AC: 2857 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	6.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729761; hg19: chr6-43804571;