9-73777969-C-A

Variant names:

• chr9-73777969-C-A
• rs4745257
• ENST00000715874.1:n.354+109G>T

Variant summary

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

The ENST00000715874.1(ENSG00000293610):​n.354+109G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,032 control chromosomes in the GnomAD database, including 54,801 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 0.84 (54801 hom., cov: 32)
• Consequence: ENSG00000293610 ENST00000715874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 2 publications found

Genes affected

ENSG00000293610 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 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
ENSG00000293610	ENST00000715874.1	n.354+109G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 126952 AN: 151914 Hom.: 54781 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.836 AC: 127029 AN: 152032 Hom.: 54801 Cov.: 32 AF XY: 0.837 AC XY: 62175 AN XY: 74326

African (AFR) AF: 0.611 AC: 25303 AN: 41424

American (AMR) AF: 0.841 AC: 12800 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3288 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3895 AN: 5160

South Asian (SAS) AF: 0.850 AC: 4097 AN: 4820

European-Finnish (FIN) AF: 0.956 AC: 10147 AN: 10610

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64520 AN: 68010

Other (OTH) AF: 0.855 AC: 1805 AN: 2110

Alfa AF: 0.916 Hom.: 100972

Bravo AF: 0.814

Asia WGS AF: 0.787 AC: 2737 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	0.37
DANN	Benign	0.55
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4745257; hg19: chr9-76392885;