chr4-119854993-C-T

Variant names:

• chr4-119854993-C-T
• rs9307481

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;