9-73794510-A-G

Variant names:

• chr9-73794510-A-G
• rs1379911
• ENST00000715874.1:n.208-16286T>C

Variant summary

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

The ENST00000715874.1(ENSG00000293610):​n.208-16286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 151,360 control chromosomes in the GnomAD database, including 59,002 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 0.88 (59002 hom., cov: 30)
• Consequence: ENSG00000293610 ENST00000715874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 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.208-16286T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.877 AC: 132606 AN: 151244 Hom.: 58978 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.942

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.877 AC: 132682 AN: 151360 Hom.: 59002 Cov.: 30 AF XY: 0.878 AC XY: 64922 AN XY: 73954

African (AFR) AF: 0.715 AC: 29608 AN: 41384

American (AMR) AF: 0.866 AC: 13111 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3281 AN: 3462

East Asian (EAS) AF: 0.950 AC: 4901 AN: 5160

South Asian (SAS) AF: 0.884 AC: 4265 AN: 4824

European-Finnish (FIN) AF: 0.958 AC: 10071 AN: 10514

Middle Eastern (MID) AF: 0.941 AC: 273 AN: 290

European-Non Finnish (NFE) AF: 0.953 AC: 64382 AN: 67576

Other (OTH) AF: 0.899 AC: 1888 AN: 2100

Alfa AF: 0.904 Hom.: 7695

Bravo AF: 0.862

Asia WGS AF: 0.873 AC: 2995 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1379911; hg19: chr9-76409426;