rs11168068

Variant names:

• chr5-148824558-C-T
• rs11168068

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 0.598 in 151,608 control chromosomes in the GnomAD database, including 27,541 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 0.60 (27541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.598 AC: 90636 AN: 151490 Hom.: 27522 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.598 AC: 90700 AN: 151608 Hom.: 27541 Cov.: 31 AF XY: 0.606 AC XY: 44888 AN XY: 74100

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.630

Alfa AF: 0.585 Hom.: 11392

Bravo AF: 0.599

Asia WGS AF: 0.747 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11168068; hg19: chr5-148204121;