rs752274

Variant names:

• chr9-98937329-C-T
• rs752274

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 0.0671 in 152,224 control chromosomes in the GnomAD database, including 641 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 0.067 (641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

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 = 0.15 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

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10167 AN: 152106 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0671 AC: 10215 AN: 152224 Hom.: 641 Cov.: 32 AF XY: 0.0731 AC XY: 5442 AN XY: 74432

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0424 Hom.: 43

Bravo AF: 0.0792

Asia WGS AF: 0.108 AC: 375 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	0.69
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752274; hg19: chr9-101699611;