rs11168327

Variant names:

• chr12-47952192-C-T
• rs11168327

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 0.375 in 152,054 control chromosomes in the GnomAD database, including 12,274 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 0.38 (12274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 7 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 = 0.574 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: 0.375 AC: 56960 AN: 151936 Hom.: 12252 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.375 AC: 57023 AN: 152054 Hom.: 12274 Cov.: 32 AF XY: 0.375 AC XY: 27872 AN XY: 74352

African (AFR) AF: 0.562 AC: 23307 AN: 41438

American (AMR) AF: 0.458 AC: 6994 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3056 AN: 5164

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2539 AN: 10602

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17507 AN: 67962

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.304 Hom.: 10015

Bravo AF: 0.401

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs11168327; hg19: chr12-48345975;