rs17700633

Variant names:

• chr18-60262199-G-A
• rs17700633

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;