18-65450257-T-G

Variant names:

• chr18-65450257-T-G
• rs2850699

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 0.444 in 151,724 control chromosomes in the GnomAD database, including 15,072 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 0.44 (15072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67294 AN: 151606 Hom.: 15055 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.444 AC: 67348 AN: 151724 Hom.: 15072 Cov.: 32 AF XY: 0.444 AC XY: 32893 AN XY: 74116

African (AFR) AF: 0.440 AC: 18193 AN: 41374

American (AMR) AF: 0.399 AC: 6082 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3466

East Asian (EAS) AF: 0.595 AC: 3059 AN: 5140

South Asian (SAS) AF: 0.462 AC: 2220 AN: 4806

European-Finnish (FIN) AF: 0.402 AC: 4248 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 29983 AN: 67852

Other (OTH) AF: 0.447 AC: 939 AN: 2102

Alfa AF: 0.328 Hom.: 1054

Bravo AF: 0.450

Asia WGS AF: 0.454 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.90
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2850699; hg19: chr18-63117493;