12-11350271-A-G

Variant names:

• chr12-11350271-A-G
• rs2059764

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 0.415 in 152,088 control chromosomes in the GnomAD database, including 15,382 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 0.42 (15382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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: 0.416 AC: 63146 AN: 151970 Hom.: 15388 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.415 AC: 63136 AN: 152088 Hom.: 15382 Cov.: 32 AF XY: 0.416 AC XY: 30958 AN XY: 74338

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.433

Alfa AF: 0.517 Hom.: 30421

Bravo AF: 0.395

Asia WGS AF: 0.364 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059764; hg19: chr12-11503205;