chr11-5173580-A-G

Variant names:

• chr11-5173580-A-G
• rs4128713

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 0.0499 in 152,204 control chromosomes in the GnomAD database, including 537 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 0.050 (537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.0497 AC: 7564 AN: 152086 Hom.: 534 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0499 AC: 7595 AN: 152204 Hom.: 537 Cov.: 33 AF XY: 0.0477 AC XY: 3552 AN XY: 74428

African (AFR) AF: 0.154 AC: 6391 AN: 41528

American (AMR) AF: 0.0333 AC: 510 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4818

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.00589 AC: 400 AN: 67962

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0115 Hom.: 8

Bravo AF: 0.0551

Asia WGS AF: 0.0170 AC: 59 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4128713; hg19: chr11-5194810;