rs73511817

Variant names:

• chr9-108383745-C-A
• rs73511817
• ENST00000826308.1:n.98-8149G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000826308.1(ENSG00000307437):​n.98-8149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,028 control chromosomes in the GnomAD database, including 185 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 0.042 (185 hom., cov: 32)
• Consequence: ENSG00000307437 ENST00000826308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 0 publications found

Genes affected

ENSG00000307437 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826308.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307437	ENST00000826308.1		n.98-8149G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6394 AN: 151910 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0421 AC: 6401 AN: 152028 Hom.: 185 Cov.: 32 AF XY: 0.0429 AC XY: 3186 AN XY: 74312

African (AFR) AF: 0.0686 AC: 2843 AN: 41434

American (AMR) AF: 0.0371 AC: 566 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0752 AC: 362 AN: 4812

European-Finnish (FIN) AF: 0.0204 AC: 215 AN: 10560

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0313 AC: 2129 AN: 67970

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0339 Hom.: 146

Bravo AF: 0.0432

Asia WGS AF: 0.0280 AC: 98 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	21
DANN	Benign	0.55
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs73511817;

hg19: chr9-111146025;