rs178503

Variant names:

• chr11-44061381-G-A
• rs178503

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 0.485 in 151,926 control chromosomes in the GnomAD database, including 18,021 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 0.49 (18021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.485 AC: 73656 AN: 151808 Hom.: 18007 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.485 AC: 73702 AN: 151926 Hom.: 18021 Cov.: 32 AF XY: 0.483 AC XY: 35887 AN XY: 74238

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.463

Alfa AF: 0.502 Hom.: 39227

Bravo AF: 0.480

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs178503; hg19: chr11-44082931;