rs1389338

Variant names:

• chr4-133550786-G-C
• rs1389338

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 0.619 in 151,926 control chromosomes in the GnomAD database, including 29,236 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 0.62 (29236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 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: 0.619 AC: 93924 AN: 151808 Hom.: 29214 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.619 AC: 93991 AN: 151926 Hom.: 29236 Cov.: 32 AF XY: 0.617 AC XY: 45819 AN XY: 74248

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.597

Alfa AF: 0.620 Hom.: 3687

Bravo AF: 0.615

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0080
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1389338; hg19: chr4-134471941;