rs11829144

Variant names:

• chr12-10197434-T-C
• rs11829144

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 0.0703 in 152,196 control chromosomes in the GnomAD database, including 397 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 0.070 (397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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 = 0.0971 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: 0.0702 AC: 10681 AN: 152080 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0823

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0703 AC: 10694 AN: 152196 Hom.: 397 Cov.: 32 AF XY: 0.0697 AC XY: 5183 AN XY: 74412

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0823

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0624 Hom.: 241

Bravo AF: 0.0716

Asia WGS AF: 0.102 AC: 354 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	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11829144; hg19: chr12-10350033;