rs2412865

Positions:

• chr4-58067689-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 0.29 in 151,916 control chromosomes in the GnomAD database, including 6,636 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 0.29 (6636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44005 AN: 151798 Hom.: 6639 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.290 AC: 44001 AN: 151916 Hom.: 6636 Cov.: 32 AF XY: 0.288 AC XY: 21348 AN XY: 74252

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.310

Alfa AF: 0.177 Hom.: 341

Bravo AF: 0.286

Asia WGS AF: 0.237 AC: 825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2412865; hg19: chr4-58933855;