rs11829144

Variant names:

• chr12-10197434-T-C
• rs11829144

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0915 AC: 3799 AN: 41534

American (AMR) AF: 0.0582 AC: 889 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 285 AN: 3464

East Asian (EAS) AF: 0.0763 AC: 396 AN: 5192

South Asian (SAS) AF: 0.105 AC: 505 AN: 4826

European-Finnish (FIN) AF: 0.0567 AC: 600 AN: 10584

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3958 AN: 68002

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0633 Hom.: 310

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
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11829144; hg19: chr12-10350033;