11-5179090-A-C

Variant names:

• chr11-5179090-A-C
• rs4910726

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 0.223 in 152,158 control chromosomes in the GnomAD database, including 4,018 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 0.22 (4018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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: 0.223 AC: 33935 AN: 152040 Hom.: 4009 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.223 AC: 33980 AN: 152158 Hom.: 4018 Cov.: 32 AF XY: 0.222 AC XY: 16512 AN XY: 74372

African (AFR) AF: 0.196 AC: 8147 AN: 41498

American (AMR) AF: 0.255 AC: 3898 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3472

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4814

European-Finnish (FIN) AF: 0.207 AC: 2196 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16663 AN: 68006

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.191 Hom.: 769

Bravo AF: 0.225

Asia WGS AF: 0.167 AC: 578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.26
PhyloP100		-0.28
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: rs4910726; hg19: chr11-5200320;