rs675566

chr18-40999812-A-Cchr18-40999812-A-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 0.236 in 151,798 control chromosomes in the GnomAD database, including 5,151 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 0.24 (5151 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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: 0.236 AC: 35808 AN: 151680 Hom.: 5154 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.236 AC: 35803 AN: 151798 Hom.: 5151 Cov.: 32 AF XY: 0.236 AC XY: 17546 AN XY: 74194

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.247

Alfa AF: 0.300 Hom.: 9802

Bravo AF: 0.222

Asia WGS AF: 0.0990 AC: 342 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs675566; hg19: chr18-38579776;