ENST00000815379.1:n.139+163A>G

Variant names:

• chr9-27075717-A-G
• rs1577330
• ENST00000815379.1:n.139+163A>G

Variant summary

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

The ENST00000815379.1(ENSG00000306113):​n.139+163A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,026 control chromosomes in the GnomAD database, including 8,924 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 0.32 (8924 hom., cov: 32)
• Consequence: ENSG00000306113 ENST00000815379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 5 publications found

Genes affected

ENSG00000306113 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306113	ENST00000815379.1	n.139+163A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49064 AN: 151908 Hom.: 8890 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.323 AC: 49161 AN: 152026 Hom.: 8924 Cov.: 32 AF XY: 0.332 AC XY: 24708 AN XY: 74314

African (AFR) AF: 0.408 AC: 16919 AN: 41454

American (AMR) AF: 0.314 AC: 4805 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3702 AN: 5134

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4820

European-Finnish (FIN) AF: 0.305 AC: 3224 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16076 AN: 67972

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.264 Hom.: 906

Bravo AF: 0.328

Asia WGS AF: 0.554 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1577330; hg19: chr9-27075715;