rs2412865

Variant names:

• chr4-58067689-A-G
• rs2412865

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 0.29 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.237 AC: 9834 AN: 41476

American (AMR) AF: 0.281 AC: 4267 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3472

East Asian (EAS) AF: 0.127 AC: 651 AN: 5142

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4812

European-Finnish (FIN) AF: 0.275 AC: 2913 AN: 10586

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22059 AN: 67904

Other (OTH) AF: 0.310 AC: 654 AN: 2108

Alfa AF: 0.182 Hom.: 366

Bravo AF: 0.286

Asia WGS AF: 0.237 AC: 825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.49
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2412865; hg19: chr4-58933855;