rs17700633

Positions:

• chr18-60262199-G-A

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 0.278 in 152,048 control chromosomes in the GnomAD database, including 6,160 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 (6160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42205 AN: 151930 Hom.: 6157 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.278 AC: 42235 AN: 152048 Hom.: 6160 Cov.: 32 AF XY: 0.270 AC XY: 20093 AN XY: 74312

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.256

Alfa AF: 0.277 Hom.: 1062

Bravo AF: 0.274

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17700633; hg19: chr18-57929432;