chr5-72388058-G-A

Variant names:

• chr5-72388058-G-A
• rs9293289

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 0.242 in 152,072 control chromosomes in the GnomAD database, including 5,304 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 0.24 (5304 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.242 AC: 36817 AN: 151956 Hom.: 5307 Cov.: 33

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.242 AC: 36821 AN: 152072 Hom.: 5304 Cov.: 33 AF XY: 0.250 AC XY: 18555 AN XY: 74334

African (AFR) AF: 0.0854 AC: 3543 AN: 41482

American (AMR) AF: 0.247 AC: 3779 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2642 AN: 5178

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4017 AN: 10544

Middle Eastern (MID) AF: 0.231 AC: 67 AN: 290

European-Non Finnish (NFE) AF: 0.284 AC: 19296 AN: 67984

Other (OTH) AF: 0.260 AC: 548 AN: 2106

Alfa AF: 0.266 Hom.: 17719

Bravo AF: 0.226

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.40
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9293289; hg19: chr5-71683885; COSMIC: COSV60154405;