chr5-132071351-A-G

Variant names:

• chr5-132071351-A-G
• rs25879

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 0.27 in 147,832 control chromosomes in the GnomAD database, including 5,768 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 0.27 (5768 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.270 AC: 39811 AN: 147708 Hom.: 5751 Cov.: 28

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.270 AC: 39861 AN: 147832 Hom.: 5768 Cov.: 28 AF XY: 0.276 AC XY: 19911 AN XY: 72080

African (AFR) AF: 0.301 AC: 12085 AN: 40138

American (AMR) AF: 0.228 AC: 3409 AN: 14920

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 973 AN: 3412

East Asian (EAS) AF: 0.599 AC: 2917 AN: 4866

South Asian (SAS) AF: 0.263 AC: 1162 AN: 4416

European-Finnish (FIN) AF: 0.397 AC: 3947 AN: 9948

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14652 AN: 66862

Other (OTH) AF: 0.258 AC: 537 AN: 2080

Alfa AF: 0.228 Hom.: 8056

Bravo AF: 0.260

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.79
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs25879; hg19: chr5-131407044;