ENST00000609858.1:n.243T>G

Variant names:

• chr7-7620114-T-G
• rs1476647
• ENST00000609858.1:n.243T>G

Variant summary

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

The ENST00000609858.1(ENSG00000272745):​n.243T>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 0.753 in 151,934 control chromosomes in the GnomAD database, including 43,736 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 0.75 (43735 hom., cov: 30)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000272745 ENST00000609858.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 4 publications found

Genes affected

ENSG00000272745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609858.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272745	ENST00000609858.1	TSL:6	n.243T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114303 AN: 151814 Hom.: 43724 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.755

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.753 AC: 114345 AN: 151932 Hom.: 43735 Cov.: 30 AF XY: 0.750 AC XY: 55703 AN XY: 74242

African (AFR) AF: 0.617 AC: 25564 AN: 41426

American (AMR) AF: 0.815 AC: 12447 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2519 AN: 3462

East Asian (EAS) AF: 0.594 AC: 3064 AN: 5158

South Asian (SAS) AF: 0.784 AC: 3741 AN: 4772

European-Finnish (FIN) AF: 0.776 AC: 8190 AN: 10554

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56197 AN: 67982

Other (OTH) AF: 0.753 AC: 1587 AN: 2108

Alfa AF: 0.800 Hom.: 39051

Bravo AF: 0.751

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs1476647; hg19: chr7-7659745;