rs11065611

Positions:

• chr12-110266682-C-T

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 0.0564 in 152,322 control chromosomes in the GnomAD database, including 326 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 0.056 (326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.0563 AC: 8576 AN: 152204 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0564 AC: 8590 AN: 152322 Hom.: 326 Cov.: 32 AF XY: 0.0571 AC XY: 4255 AN XY: 74476

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0751

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0697 Hom.: 947

Bravo AF: 0.0523

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11065611; hg19: chr12-110704487;