ENST00000663906.1:n.178A>G

Variant names:

• chr6-47397221-T-C
• rs4715005
• ENST00000663906.1:n.178A>G

Variant summary

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

The ENST00000663906.1(ENSG00000287485):​n.178A>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 0.722 in 152,128 control chromosomes in the GnomAD database, including 40,729 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 0.72 (40729 hom., cov: 33)
• Consequence: ENSG00000287485 ENST00000663906.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.48
• Publications: 5 publications found

Genes affected

ENSG00000287485 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663906.1. 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
	ENSG00000287485	ENST00000663906.1		n.178A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000287485	ENST00000741072.1		n.822-44A>G		intron	N/A
	ENSG00000287485	ENST00000741073.1		n.272-44A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109736 AN: 152010 Hom.: 40702 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.722 AC: 109805 AN: 152128 Hom.: 40729 Cov.: 33 AF XY: 0.726 AC XY: 54026 AN XY: 74366

African (AFR) AF: 0.537 AC: 22272 AN: 41468

American (AMR) AF: 0.776 AC: 11855 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2543 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4805 AN: 5180

South Asian (SAS) AF: 0.749 AC: 3615 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8999 AN: 10594

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53410 AN: 67988

Other (OTH) AF: 0.725 AC: 1529 AN: 2110

Alfa AF: 0.746 Hom.: 80290

Bravo AF: 0.708

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.33
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs4715005; hg19: chr6-47364957;