chr9-107469582-A-G

Variant names:

• chr9-107469582-A-G
• rs1819730
• ENST00000837839.1:n.424-10688A>G

Variant summary

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

The ENST00000837839.1(ENSG00000309014):​n.424-10688A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,228 control chromosomes in the GnomAD database, including 2,635 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 0.17 (2635 hom., cov: 32)
• Consequence: ENSG00000309014 ENST00000837839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.812
• Publications: 6 publications found

Genes affected

ENSG00000309014 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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
ENSG00000309014	ENST00000837839.1	n.424-10688A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26567 AN: 152110 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.175 AC: 26587 AN: 152228 Hom.: 2635 Cov.: 32 AF XY: 0.171 AC XY: 12725 AN XY: 74432

African (AFR) AF: 0.267 AC: 11076 AN: 41506

American (AMR) AF: 0.126 AC: 1934 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5188

South Asian (SAS) AF: 0.154 AC: 744 AN: 4828

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10604

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10386 AN: 68010

Other (OTH) AF: 0.182 AC: 386 AN: 2116

Alfa AF: 0.158 Hom.: 3314

Bravo AF: 0.177

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.2
DANN	Benign	0.46
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1819730; hg19: chr9-110231863;