chr5-150802872-A-G

Variant names:

• chr5-150802872-A-G
• rs2112637

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 0.202 in 152,164 control chromosomes in the GnomAD database, including 4,115 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 0.20 (4115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30790 AN: 152046 Hom.: 4116 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.202 AC: 30803 AN: 152164 Hom.: 4115 Cov.: 32 AF XY: 0.206 AC XY: 15303 AN XY: 74410

African (AFR) AF: 0.291 AC: 12085 AN: 41486

American (AMR) AF: 0.172 AC: 2629 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3466

East Asian (EAS) AF: 0.633 AC: 3275 AN: 5170

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10612

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8771 AN: 67998

Other (OTH) AF: 0.218 AC: 462 AN: 2116

Alfa AF: 0.157 Hom.: 4321

Bravo AF: 0.213

Asia WGS AF: 0.421 AC: 1465 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	0.0090
DANN	Benign	0.32
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2112637; hg19: chr5-150182434;