rs12800752

Variant names:

• chr11-100535909-T-C
• rs12800752

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0467 in 152,260 control chromosomes in the GnomAD database, including 303 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 0.047 (303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 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: 0.0467 AC: 7101 AN: 152144 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0415

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

GnomAD4 genome AF: 0.0467 AC: 7107 AN: 152260 Hom.: 303 Cov.: 32 AF XY: 0.0481 AC XY: 3581 AN XY: 74458

African (AFR) AF: 0.0999 AC: 4151 AN: 41548

American (AMR) AF: 0.0499 AC: 763 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3470

East Asian (EAS) AF: 0.126 AC: 654 AN: 5172

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4828

European-Finnish (FIN) AF: 0.0289 AC: 307 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 950 AN: 68012

Other (OTH) AF: 0.0406 AC: 86 AN: 2116

Alfa AF: 0.0452 Hom.: 149

Bravo AF: 0.0510

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12800752; hg19: chr11-100406640;