rs4313384

Positions:

• chr1-238784332-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 0.0941 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;