rs1869463

chr4-58438966-A-G

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 0.398 in 151,996 control chromosomes in the GnomAD database, including 12,817 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 0.40 (12817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.398 AC: 60476 AN: 151878 Hom.: 12781 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.398 AC: 60557 AN: 151996 Hom.: 12817 Cov.: 32 AF XY: 0.400 AC XY: 29757 AN XY: 74308

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.345

Alfa AF: 0.377 Hom.: 1958

Bravo AF: 0.408

Asia WGS AF: 0.438 AC: 1523 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	0.27
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869463; hg19: chr4-59305132;