rs4313384

Variant names:

• chr1-238784332-C-T
• rs4313384

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 0.0941 in 152,198 control chromosomes in the GnomAD database, including 894 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 0.094 (894 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 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: 0.0942 AC: 14321 AN: 152080 Hom.: 893 Cov.: 33

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0941 AC: 14326 AN: 152198 Hom.: 894 Cov.: 33 AF XY: 0.0932 AC XY: 6936 AN XY: 74392

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0904

Alfa AF: 0.123 Hom.: 1583

Bravo AF: 0.0945

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4313384; hg19: chr1-238947632;