rs633265

Positions:

• chr18-60164235-G-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 0.513 in 151,120 control chromosomes in the GnomAD database, including 21,961 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 0.51 (21961 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.513 AC: 77402 AN: 151000 Hom.: 21921 Cov.: 28

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.513 AC: 77493 AN: 151120 Hom.: 21961 Cov.: 28 AF XY: 0.508 AC XY: 37480 AN XY: 73778

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.470

Alfa AF: 0.451 Hom.: 9359

Bravo AF: 0.516

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs633265; hg19: chr18-57831468;