rs7874184

Positions:

• chr9-73692524-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73692524T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.328

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7874184; hg19: chr9-76307440;