rs633265

Variant names:

• chr18-60164235-G-T
• rs633265

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.762 AC: 31369 AN: 41144

American (AMR) AF: 0.378 AC: 5725 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1107 AN: 5108

South Asian (SAS) AF: 0.554 AC: 2644 AN: 4776

European-Finnish (FIN) AF: 0.427 AC: 4454 AN: 10434

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29517 AN: 67740

Other (OTH) AF: 0.470 AC: 988 AN: 2104

Alfa AF: 0.457 Hom.: 11077

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
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs633265; hg19: chr18-57831468;