rs729239

Positions:

• chr4-77142243-G-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 0.131 in 152,130 control chromosomes in the GnomAD database, including 2,014 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 0.13 (2014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.130 AC: 19823 AN: 152012 Hom.: 2003 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.131 AC: 19880 AN: 152130 Hom.: 2014 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74396

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.0389

Gnomad4 SAS AF: 0.0774

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.113

Alfa AF: 0.124 Hom.: 309

Bravo AF: 0.141

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.010
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729239; hg19: chr4-78063396;