rs725169

Variant names:

• chr18-61256416-C-T
• rs725169

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 0.0108 in 152,084 control chromosomes in the GnomAD database, including 24 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 0.011 (24 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.062 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: 0.0109 AC: 1649 AN: 151966 Hom.: 24 Cov.: 32

Gnomad AFR AF: 0.00844

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.00369

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00694

Gnomad OTH AF: 0.00961

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

GnomAD4 genome AF: 0.0108 AC: 1642 AN: 152084 Hom.: 24 Cov.: 32 AF XY: 0.0114 AC XY: 851 AN XY: 74348

African (AFR) AF: 0.00841 AC: 349 AN: 41494

American (AMR) AF: 0.0187 AC: 285 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3468

East Asian (EAS) AF: 0.0678 AC: 349 AN: 5146

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4810

European-Finnish (FIN) AF: 0.00369 AC: 39 AN: 10580

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00694 AC: 472 AN: 68006

Other (OTH) AF: 0.00951 AC: 20 AN: 2104

Alfa AF: 0.00836 Hom.: 2

Bravo AF: 0.0125

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0070
DANN	Benign	0.61
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs725169; hg19: chr18-58923649;