rs788867

Variant names:

• chr4-81228852-T-G
• rs788867

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.659 AC: 27331 AN: 41460

American (AMR) AF: 0.311 AC: 4749 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3470

East Asian (EAS) AF: 0.184 AC: 955 AN: 5184

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4822

European-Finnish (FIN) AF: 0.363 AC: 3826 AN: 10534

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21673 AN: 67974

Other (OTH) AF: 0.352 AC: 743 AN: 2108

Alfa AF: 0.396 Hom.: 1753

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs788867; hg19: chr4-82150006;