rs11168618

Variant names:

• chr12-48539450-C-T
• rs11168618

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 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0936 AC: 3890 AN: 41550

American (AMR) AF: 0.395 AC: 6026 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3468

East Asian (EAS) AF: 0.160 AC: 826 AN: 5164

South Asian (SAS) AF: 0.337 AC: 1627 AN: 4830

European-Finnish (FIN) AF: 0.439 AC: 4625 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30940 AN: 67956

Other (OTH) AF: 0.347 AC: 734 AN: 2116

Alfa AF: 0.381 Hom.: 4208

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
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs11168618; hg19: chr12-48933233;