rs739718

Positions:

• chr5-132537381-T-C
• chr5-132537381-T-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 0.114 in 152,238 control chromosomes in the GnomAD database, including 1,499 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 0.11 (1499 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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: 0.114 AC: 17314 AN: 152120 Hom.: 1492 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.114 AC: 17336 AN: 152238 Hom.: 1499 Cov.: 31 AF XY: 0.112 AC XY: 8346 AN XY: 74440

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0693 Hom.: 242

Bravo AF: 0.124

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739718; hg19: chr5-131873073;