rs7874184

Variant names:

• chr9-73692524-T-G
• rs7874184
• ENST00000715873.1:n.166-33958T>G

Variant summary

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

The ENST00000715873.1(ENSG00000232590):​n.166-33958T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,890 control chromosomes in the GnomAD database, including 9,868 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 0.36 (9868 hom., cov: 32)
• Consequence: ENSG00000232590 ENST00000715873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

ENSG00000232590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715873.1. 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
	ENSG00000232590	ENST00000715873.1		n.166-33958T>G		intron	N/A
	ENSG00000293610	ENST00000715874.1		n.354+85554A>C		intron	N/A
	ENSG00000305891	ENST00000813827.1		n.94+7340A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53989 AN: 151774 Hom.: 9854 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.356 AC: 54036 AN: 151890 Hom.: 9868 Cov.: 32 AF XY: 0.354 AC XY: 26238 AN XY: 74218

African (AFR) AF: 0.419 AC: 17349 AN: 41442

American (AMR) AF: 0.419 AC: 6384 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1552 AN: 5158

South Asian (SAS) AF: 0.281 AC: 1350 AN: 4800

European-Finnish (FIN) AF: 0.313 AC: 3303 AN: 10546

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22289 AN: 67930

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.342 Hom.: 2028

Bravo AF: 0.365

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.94
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7874184; hg19: chr9-76307440;