rs1789891

Variant names:

• chr4-99329262-C-A
• rs1789891

Your query was ambiguous. Multiple possible variants found:

• chr4-99329262-C-A
• chr4-99329262-C-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 0.128 in 152,130 control chromosomes in the GnomAD database, including 1,548 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 (1548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 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: 0.128 AC: 19467 AN: 152012 Hom.: 1540 Cov.: 33

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.128 AC: 19481 AN: 152130 Hom.: 1548 Cov.: 33 AF XY: 0.130 AC XY: 9654 AN XY: 74352

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.118

Alfa AF: 0.152 Hom.: 3947

Bravo AF: 0.120

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789891; hg19: chr4-100250419;