rs11168618

Positions:

• chr12-48539450-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 0.333 in 152,086 control chromosomes in the GnomAD database, including 10,425 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 (10425 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50587 AN: 151966 Hom.: 10425 Cov.: 31

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.333 AC: 50593 AN: 152086 Hom.: 10425 Cov.: 31 AF XY: 0.333 AC XY: 24790 AN XY: 74338

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.347

Alfa AF: 0.394 Hom.: 2174

Bravo AF: 0.321

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11168618; hg19: chr12-48933233;