9-73727490-T-C

Variant names:

• chr9-73727490-T-C
• rs11143683
• ENST00000715874.1:n.354+50588A>G

Variant summary

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

The ENST00000715874.1(ENSG00000293610):​n.354+50588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,964 control chromosomes in the GnomAD database, including 15,281 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 0.41 (15281 hom., cov: 32)
• Consequence: ENSG00000293610 ENST00000715874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 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+50588A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62505 AN: 151846 Hom.: 15282 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.411 AC: 62510 AN: 151964 Hom.: 15281 Cov.: 32 AF XY: 0.416 AC XY: 30887 AN XY: 74258

African (AFR) AF: 0.132 AC: 5481 AN: 41498

American (AMR) AF: 0.409 AC: 6224 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2239 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2753 AN: 5116

South Asian (SAS) AF: 0.527 AC: 2543 AN: 4822

European-Finnish (FIN) AF: 0.547 AC: 5786 AN: 10580

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35807 AN: 67934

Other (OTH) AF: 0.471 AC: 992 AN: 2104

Alfa AF: 0.445 Hom.: 2980

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.64
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11143683; hg19: chr9-76342406;