ENST00000806122.1:n.1139G>A

Variant names:

• chr6-104336944-C-T
• rs270678
• ENST00000806122.1:n.1139G>A

Variant summary

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

The ENST00000806122.1(ENSG00000304752):​n.1139G>A 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 0.852 in 152,112 control chromosomes in the GnomAD database, including 55,594 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 0.85 (55594 hom., cov: 31)
• Consequence: ENSG00000304752 ENST00000806122.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 2 publications found

Genes affected

ENSG00000304752 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806122.1. 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
	ENSG00000304752	ENST00000806122.1		n.1139G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129492 AN: 151994 Hom.: 55527 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.852 AC: 129619 AN: 152112 Hom.: 55594 Cov.: 31 AF XY: 0.852 AC XY: 63330 AN XY: 74338

African (AFR) AF: 0.945 AC: 39262 AN: 41530

American (AMR) AF: 0.877 AC: 13384 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2748 AN: 3464

East Asian (EAS) AF: 0.869 AC: 4490 AN: 5164

South Asian (SAS) AF: 0.799 AC: 3852 AN: 4822

European-Finnish (FIN) AF: 0.780 AC: 8224 AN: 10542

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54749 AN: 68010

Other (OTH) AF: 0.878 AC: 1857 AN: 2116

Alfa AF: 0.839 Hom.: 41374

Bravo AF: 0.866

Asia WGS AF: 0.837 AC: 2900 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs270678; hg19: chr6-104784819;