rs1791285

Variant names:

• chr18-59698951-T-C
• rs1791285

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 0.147 in 152,174 control chromosomes in the GnomAD database, including 1,671 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 0.15 (1671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 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: 0.147 AC: 22326 AN: 152056 Hom.: 1670 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.147 AC: 22334 AN: 152174 Hom.: 1671 Cov.: 32 AF XY: 0.144 AC XY: 10751 AN XY: 74414

African (AFR) AF: 0.155 AC: 6418 AN: 41502

American (AMR) AF: 0.159 AC: 2426 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.101 AC: 524 AN: 5174

South Asian (SAS) AF: 0.137 AC: 659 AN: 4820

European-Finnish (FIN) AF: 0.0826 AC: 876 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10287 AN: 68004

Other (OTH) AF: 0.156 AC: 329 AN: 2108

Alfa AF: 0.150 Hom.: 231

Bravo AF: 0.149

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.39
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs1791285; hg19: chr18-57366183;