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. The variant received -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
• Publications: 52 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0389 AC: 1615 AN: 41528

American (AMR) AF: 0.146 AC: 2235 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5178

South Asian (SAS) AF: 0.171 AC: 824 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2271 AN: 10544

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11587 AN: 67990

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.153 Hom.: 8098

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1789891; hg19: chr4-100250419;