rs308447

Variant names:

• chr4-122817391-C-T
• rs308447

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.763 AC: 31630 AN: 41476

American (AMR) AF: 0.398 AC: 6073 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.119 AC: 615 AN: 5178

South Asian (SAS) AF: 0.416 AC: 2007 AN: 4820

European-Finnish (FIN) AF: 0.253 AC: 2665 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25169 AN: 67936

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.398 Hom.: 20534

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs308447; hg19: chr4-123738546;