rs11169748

Variant names:

• chr12-51185388-A-G
• rs11169748

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 0.0585 in 152,248 control chromosomes in the GnomAD database, including 636 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 0.058 (636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.0584 AC: 8880 AN: 152130 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0585 AC: 8900 AN: 152248 Hom.: 636 Cov.: 32 AF XY: 0.0558 AC XY: 4157 AN XY: 74456

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0247 Hom.: 196

Bravo AF: 0.0652

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11169748; hg19: chr12-51579171;