5-132070740-T-G

Variant names:

• chr5-132070740-T-G
• rs721121

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 0.359 in 152,076 control chromosomes in the GnomAD database, including 10,499 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 0.36 (10499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.359 AC: 54579 AN: 151958 Hom.: 10488 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.359 AC: 54611 AN: 152076 Hom.: 10499 Cov.: 32 AF XY: 0.344 AC XY: 25569 AN XY: 74362

African (AFR) AF: 0.352 AC: 14610 AN: 41448

American (AMR) AF: 0.331 AC: 5055 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5182

South Asian (SAS) AF: 0.126 AC: 606 AN: 4818

European-Finnish (FIN) AF: 0.276 AC: 2923 AN: 10592

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28851 AN: 67954

Other (OTH) AF: 0.370 AC: 782 AN: 2114

Alfa AF: 0.256 Hom.: 689

Bravo AF: 0.368

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs721121; hg19: chr5-131406433; COSMIC: COSV51522270;