rs9307481

chr4-119854993-C-T

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 0.0918 in 152,042 control chromosomes in the GnomAD database, including 1,587 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 0.092 (1587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13927 AN: 151924 Hom.: 1581 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0565

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00686

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0918 AC: 13965 AN: 152042 Hom.: 1587 Cov.: 32 AF XY: 0.0886 AC XY: 6580 AN XY: 74308

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00666

Gnomad4 FIN AF: 0.00340

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.0454 Hom.: 125

Bravo AF: 0.106

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.052
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307481; hg19: chr4-120776148;