rs4913428

Variant names:

• chr12-68244448-C-A
• rs4913428

Your query was ambiguous. Multiple possible variants found:

• chr12-68244448-C-A
• chr12-68244448-C-G

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 0.486 in 151,872 control chromosomes in the GnomAD database, including 18,355 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 0.49 (18355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73691 AN: 151754 Hom.: 18318 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.486 AC: 73784 AN: 151872 Hom.: 18355 Cov.: 32 AF XY: 0.489 AC XY: 36283 AN XY: 74244

African (AFR) AF: 0.575 AC: 23788 AN: 41388

American (AMR) AF: 0.484 AC: 7390 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1974 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2689 AN: 5170

South Asian (SAS) AF: 0.598 AC: 2878 AN: 4812

European-Finnish (FIN) AF: 0.465 AC: 4895 AN: 10520

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28464 AN: 67944

Other (OTH) AF: 0.526 AC: 1113 AN: 2114

Alfa AF: 0.443 Hom.: 3147

Bravo AF: 0.494

Asia WGS AF: 0.595 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.3
DANN	Benign	0.80
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs4913428; hg19: chr12-68638228;