4-58438966-A-G

Variant names:

• chr4-58438966-A-G
• rs1869463

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 0.398 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.552 AC: 22890 AN: 41464

American (AMR) AF: 0.393 AC: 5990 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5158

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3387 AN: 10562

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22306 AN: 67952

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.424 Hom.: 6051

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1869463; hg19: chr4-59305132;