5-132672516-A-G

Position:

• chr5-132672516-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.038 in 145,748 control chromosomes in the GnomAD database, including 306 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 0.038 (306 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0380 AC: 5537 AN: 145636 Hom.: 305 Cov.: 26

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.00112

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.00699

Gnomad NFE AF: 0.00995

Gnomad OTH AF: 0.0313

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

GnomAD4 genome AF: 0.0380 AC: 5538 AN: 145748 Hom.: 306 Cov.: 26 AF XY: 0.0388 AC XY: 2758 AN XY: 71046

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.00118

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.00994

Gnomad4 OTH AF: 0.0310

Alfa AF: 0.0230 Hom.: 15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.074

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10065221; hg19: chr5-132008208;