rs11051970

Variant names:

• chr12-32384554-G-T
• rs11051970

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 0.333 in 147,486 control chromosomes in the GnomAD database, including 8,285 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 0.33 (8285 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 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: 0.333 AC: 49132 AN: 147374 Hom.: 8270 Cov.: 30

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.333 AC: 49181 AN: 147486 Hom.: 8285 Cov.: 30 AF XY: 0.343 AC XY: 24634 AN XY: 71834

African (AFR) AF: 0.289 AC: 11676 AN: 40428

American (AMR) AF: 0.353 AC: 5158 AN: 14602

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1003 AN: 3350

East Asian (EAS) AF: 0.467 AC: 2314 AN: 4954

South Asian (SAS) AF: 0.350 AC: 1607 AN: 4590

European-Finnish (FIN) AF: 0.469 AC: 4720 AN: 10058

Middle Eastern (MID) AF: 0.247 AC: 71 AN: 288

European-Non Finnish (NFE) AF: 0.326 AC: 21624 AN: 66302

Other (OTH) AF: 0.343 AC: 698 AN: 2034

Alfa AF: 0.322 Hom.: 21967

Bravo AF: 0.320

Asia WGS AF: 0.384 AC: 1307 AN: 3402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs11051970; hg19: chr12-32537488;