rs76270203

Variant names:

• chr12-113499191-A-C
• rs76270203

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;