18-65250633-A-T

Variant names:

• chr18-65250633-A-T
• rs563754

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 0.79 in 152,168 control chromosomes in the GnomAD database, including 48,239 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 0.79 (48239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.790 AC: 120135 AN: 152048 Hom.: 48181 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.790 AC: 120257 AN: 152168 Hom.: 48239 Cov.: 32 AF XY: 0.789 AC XY: 58677 AN XY: 74394

African (AFR) AF: 0.930 AC: 38638 AN: 41538

American (AMR) AF: 0.817 AC: 12493 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2605 AN: 3466

East Asian (EAS) AF: 0.572 AC: 2956 AN: 5164

South Asian (SAS) AF: 0.736 AC: 3557 AN: 4830

European-Finnish (FIN) AF: 0.698 AC: 7388 AN: 10584

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50070 AN: 67988

Other (OTH) AF: 0.802 AC: 1693 AN: 2110

Alfa AF: 0.663 Hom.: 2117

Bravo AF: 0.806

Asia WGS AF: 0.679 AC: 2359 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs563754; hg19: chr18-62917869;