rs12120353

chr1-4560936-C-Achr1-4560936-C-T

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 0.207 in 152,026 control chromosomes in the GnomAD database, including 3,380 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 0.21 (3380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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: 0.207 AC: 31511 AN: 151908 Hom.: 3381 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.207 AC: 31522 AN: 152026 Hom.: 3380 Cov.: 32 AF XY: 0.209 AC XY: 15527 AN XY: 74310

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0111

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.195

Alfa AF: 0.214 Hom.: 7242

Bravo AF: 0.200

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.15
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12120353; hg19: chr1-4620996; COSMIC: COSV59920009;