rs308447

chr4-122817391-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 0.468 in 151,996 control chromosomes in the GnomAD database, including 19,524 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 0.47 (19524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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: 0.468 AC: 71019 AN: 151880 Hom.: 19480 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.468 AC: 71124 AN: 151996 Hom.: 19524 Cov.: 32 AF XY: 0.458 AC XY: 34004 AN XY: 74318

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.456

Alfa AF: 0.392 Hom.: 15262

Bravo AF: 0.490

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.31
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308447; hg19: chr4-123738546;