rs2472527

Variant names:

• chr11-5140794-A-G
• rs2472527

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 0.18 in 152,230 control chromosomes in the GnomAD database, including 2,955 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 0.18 (2955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.363 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: 0.180 AC: 27417 AN: 152112 Hom.: 2951 Cov.: 33

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.180 AC: 27430 AN: 152230 Hom.: 2955 Cov.: 33 AF XY: 0.183 AC XY: 13655 AN XY: 74438

African (AFR) AF: 0.0697 AC: 2896 AN: 41568

American (AMR) AF: 0.213 AC: 3258 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 564 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1949 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1164 AN: 4824

European-Finnish (FIN) AF: 0.212 AC: 2239 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14870 AN: 68002

Other (OTH) AF: 0.178 AC: 377 AN: 2114

Alfa AF: 0.210 Hom.: 1839

Bravo AF: 0.175

Asia WGS AF: 0.321 AC: 1112 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2472527; hg19: chr11-5162024;