5-132672952-T-G

Variant names:

• chr5-132672952-T-G
• rs2243248

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 0.0964 in 152,050 control chromosomes in the GnomAD database, including 865 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 0.096 (865 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 163 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 (AFR) allele frequency at 95% confidence interval = 0.155 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: 0.0961 AC: 14608 AN: 151930 Hom.: 854 Cov.: 30

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0964 AC: 14662 AN: 152050 Hom.: 865 Cov.: 30 AF XY: 0.0963 AC XY: 7155 AN XY: 74334

African (AFR) AF: 0.158 AC: 6549 AN: 41442

American (AMR) AF: 0.109 AC: 1661 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.0646 AC: 332 AN: 5142

South Asian (SAS) AF: 0.122 AC: 589 AN: 4824

European-Finnish (FIN) AF: 0.0356 AC: 377 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0672 AC: 4566 AN: 67980

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.0781 Hom.: 971

Bravo AF: 0.106

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.49
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2243248; hg19: chr5-132008644;