rs11065987

Positions:

• chr12-111634620-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 0.287 in 151,942 control chromosomes in the GnomAD database, including 8,687 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 0.29 (8687 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43684 AN: 151822 Hom.: 8691 Cov.: 30

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.287 AC: 43665 AN: 151942 Hom.: 8687 Cov.: 30 AF XY: 0.279 AC XY: 20691 AN XY: 74264

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.318

Alfa AF: 0.403 Hom.: 30512

Bravo AF: 0.275

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11065987; hg19: chr12-112072424;