4-107477030-C-T

Variant names:

• chr4-107477030-C-T
• rs12498793

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 0.713 in 152,102 control chromosomes in the GnomAD database, including 38,744 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 0.71 (38744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 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: 0.713 AC: 108405 AN: 151984 Hom.: 38710 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.713 AC: 108489 AN: 152102 Hom.: 38744 Cov.: 32 AF XY: 0.717 AC XY: 53281 AN XY: 74356

African (AFR) AF: 0.697 AC: 28899 AN: 41478

American (AMR) AF: 0.710 AC: 10852 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4151 AN: 5172

South Asian (SAS) AF: 0.785 AC: 3780 AN: 4818

European-Finnish (FIN) AF: 0.766 AC: 8108 AN: 10582

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.708 AC: 48132 AN: 67990

Other (OTH) AF: 0.706 AC: 1489 AN: 2110

Alfa AF: 0.713 Hom.: 4847

Bravo AF: 0.705

Asia WGS AF: 0.815 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs12498793; hg19: chr4-108398187;