rs1789105

Variant names:

• chr18-77153044-A-G
• rs1789105

Your query was ambiguous. Multiple possible variants found:

• chr18-77153044-A-G
• chr18-77153044-A-T

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 0.276 in 152,082 control chromosomes in the GnomAD database, including 6,298 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 0.28 (6298 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 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: 0.276 AC: 41892 AN: 151964 Hom.: 6294 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.276 AC: 41912 AN: 152082 Hom.: 6298 Cov.: 33 AF XY: 0.282 AC XY: 20996 AN XY: 74380

African (AFR) AF: 0.362 AC: 15010 AN: 41452

American (AMR) AF: 0.344 AC: 5262 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2049 AN: 5178

South Asian (SAS) AF: 0.423 AC: 2042 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2906 AN: 10566

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12641 AN: 67992

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.218 Hom.: 2413

Bravo AF: 0.285

Asia WGS AF: 0.439 AC: 1525 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	4.1
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1789105; hg19: chr18-74865000;