6-43836834-T-G

Variant names:

• chr6-43836834-T-G
• rs729761
• ENST00000720677.1:n.192T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000720677.1(ENSG00000294041):​n.192T>G variant causes a non coding transcript exon 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: ENSG00000294041 ENST00000720677.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 46 publications found

Genes affected

ENSG00000294041 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294041	ENST00000720677.1		n.192T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000294041	ENST00000720678.1		n.185T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000283573	ENST00000637813.1	TSL:4	n.366-5677T>G		intron	N/A

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

African (AFR) AF: 0.879 AC: 36392 AN: 41400

American (AMR) AF: 0.825 AC: 12593 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2604 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4509 AN: 5138

South Asian (SAS) AF: 0.806 AC: 3851 AN: 4778

European-Finnish (FIN) AF: 0.708 AC: 7456 AN: 10538

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48914 AN: 67912

Other (OTH) AF: 0.769 AC: 1622 AN: 2110

Alfa AF: 0.749 Hom.: 71686

Bravo AF: 0.794

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.45
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs729761; hg19: chr6-43804571;