chr4-107477030-C-T

Variant names:

• chr4-107477030-C-T
• rs12498793

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 0.713 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.713 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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.706

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12498793; hg19: chr4-108398187;