ENST00000838107.1:n.329-1375A>G

Variant names:

• chr8-12834362-T-C
• rs17120471
• ENST00000838107.1:n.329-1375A>G

Variant summary

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

The ENST00000838107.1(ENSG00000309058):​n.329-1375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,234 control chromosomes in the GnomAD database, including 1,922 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 0.15 (1922 hom., cov: 33)
• Consequence: ENSG00000309058 ENST00000838107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 5 publications found

Genes affected

ENSG00000309058 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838107.1. 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
	ENSG00000309058	ENST00000838107.1		n.329-1375A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22621 AN: 152116 Hom.: 1914 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.149 AC: 22649 AN: 152234 Hom.: 1922 Cov.: 33 AF XY: 0.150 AC XY: 11196 AN XY: 74438

African (AFR) AF: 0.178 AC: 7381 AN: 41526

American (AMR) AF: 0.225 AC: 3436 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5182

South Asian (SAS) AF: 0.200 AC: 962 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10608

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7551 AN: 68008

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.156 Hom.: 1293

Bravo AF: 0.160

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs17120471; hg19: chr8-12691871;