rs725169

chr18-61256416-C-T

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 0.0108 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00841

Gnomad4 AMR AF: 0.0187

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0678

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.00369

Gnomad4 NFE AF: 0.00694

Gnomad4 OTH AF: 0.00951

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725169; hg19: chr18-58923649;