rs788867

chr4-81228852-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 0.408 in 152,024 control chromosomes in the GnomAD database, including 14,687 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 0.41 (14687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.408 AC: 61907 AN: 151906 Hom.: 14659 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.408 AC: 61988 AN: 152024 Hom.: 14687 Cov.: 32 AF XY: 0.403 AC XY: 29940 AN XY: 74326

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.352

Alfa AF: 0.386 Hom.: 1585

Bravo AF: 0.415

Asia WGS AF: 0.225 AC: 782 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.1
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: rs788867; hg19: chr4-82150006;