rs719756

chr5-42725527-T-A

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 0.454 in 152,030 control chromosomes in the GnomAD database, including 15,874 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 0.45 (15874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.454 AC: 69043 AN: 151912 Hom.: 15881 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.454 AC: 69056 AN: 152030 Hom.: 15874 Cov.: 32 AF XY: 0.454 AC XY: 33746 AN XY: 74294

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.457

Alfa AF: 0.452 Hom.: 1930

Bravo AF: 0.458

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.9
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719756; hg19: chr5-42725629;