chr11-5044857-A-G

Variant names:

• chr11-5044857-A-G
• rs1378736

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 0.512 in 151,868 control chromosomes in the GnomAD database, including 20,182 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 0.51 (20182 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77658 AN: 151752 Hom.: 20148 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.512 AC: 77733 AN: 151868 Hom.: 20182 Cov.: 31 AF XY: 0.510 AC XY: 37825 AN XY: 74232

African (AFR) AF: 0.567 AC: 23452 AN: 41396

American (AMR) AF: 0.522 AC: 7953 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5164

South Asian (SAS) AF: 0.526 AC: 2537 AN: 4822

European-Finnish (FIN) AF: 0.480 AC: 5070 AN: 10572

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33676 AN: 67886

Other (OTH) AF: 0.528 AC: 1112 AN: 2106

Alfa AF: 0.508 Hom.: 32929

Bravo AF: 0.520

Asia WGS AF: 0.414 AC: 1438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1378736; hg19: chr11-5066087;