rs4298948

chr12-121838349-C-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 0.0672 in 152,104 control chromosomes in the GnomAD database, including 559 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 0.067 (559 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10185 AN: 151986 Hom.: 556 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0359

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0672 AC: 10223 AN: 152104 Hom.: 559 Cov.: 31 AF XY: 0.0635 AC XY: 4722 AN XY: 74354

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0358

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0449

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0645 Hom.: 46

Bravo AF: 0.0717

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4298948; hg19: chr12-122276255;