rs178503

Variant names:

• chr11-44061381-G-A
• rs178503

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 0.485 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.462 AC: 19131 AN: 41398

American (AMR) AF: 0.413 AC: 6314 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3218 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4820

European-Finnish (FIN) AF: 0.487 AC: 5134 AN: 10532

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34285 AN: 67946

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.499 Hom.: 60567

Bravo AF: 0.480

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.36
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs178503; hg19: chr11-44082931;