rs11050038

chr12-29105394-A-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 0.163 in 152,180 control chromosomes in the GnomAD database, including 2,111 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 0.16 (2111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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: 0.163 AC: 24716 AN: 152060 Hom.: 2108 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.163 AC: 24739 AN: 152180 Hom.: 2111 Cov.: 32 AF XY: 0.158 AC XY: 11783 AN XY: 74408

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.153

Alfa AF: 0.176 Hom.: 4022

Bravo AF: 0.160

Asia WGS AF: 0.173 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.3
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11050038; hg19: chr12-29258327;