ENST00000790430.1:n.674A>G

Variant names:

• chr3-149225477-A-G
• rs11708215
• ENST00000790430.1:n.674A>G

Variant summary

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

The ENST00000790430.1(ENSG00000286714):​n.674A>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 0.195 in 152,100 control chromosomes in the GnomAD database, including 3,039 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 0.19 (3039 hom., cov: 32)
• Consequence: ENSG00000286714 ENST00000790430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 10 publications found

Genes affected

ENSG00000286714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790430.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286714	ENST00000790430.1		n.674A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286714	ENST00000663884.2		n.309+101A>G		intron	N/A
	ENSG00000286714	ENST00000790417.1		n.61+101A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29594 AN: 151982 Hom.: 3030 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.195 AC: 29623 AN: 152100 Hom.: 3039 Cov.: 32 AF XY: 0.198 AC XY: 14743 AN XY: 74370

African (AFR) AF: 0.149 AC: 6159 AN: 41472

American (AMR) AF: 0.213 AC: 3257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1697 AN: 5160

South Asian (SAS) AF: 0.222 AC: 1065 AN: 4808

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10578

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13630 AN: 68002

Other (OTH) AF: 0.212 AC: 448 AN: 2116

Alfa AF: 0.196 Hom.: 1602

Bravo AF: 0.192

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.50
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs11708215; hg19: chr3-148943264;