rs76270203

chr12-113499191-A-C

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 0.0264 in 152,246 control chromosomes in the GnomAD database, including 87 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 0.026 (87 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0622 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: 0.0263 AC: 4002 AN: 152128 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00770

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0264 AC: 4017 AN: 152246 Hom.: 87 Cov.: 32 AF XY: 0.0277 AC XY: 2061 AN XY: 74446

Gnomad4 AFR AF: 0.00770

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0399

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0262 Hom.: 11

Bravo AF: 0.0250

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.16
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76270203; hg19: chr12-113936996;