rs62090893

Variant names:

• chr18-75338379-G-A
• rs62090893

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 0.096 in 152,286 control chromosomes in the GnomAD database, including 885 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 0.096 (885 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14601 AN: 152168 Hom.: 880 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.0960 AC: 14625 AN: 152286 Hom.: 885 Cov.: 33 AF XY: 0.0969 AC XY: 7214 AN XY: 74468

African (AFR) AF: 0.156 AC: 6464 AN: 41528

American (AMR) AF: 0.0524 AC: 802 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.0942 AC: 489 AN: 5190

South Asian (SAS) AF: 0.125 AC: 602 AN: 4820

European-Finnish (FIN) AF: 0.0879 AC: 934 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0719 AC: 4893 AN: 68022

Other (OTH) AF: 0.0832 AC: 176 AN: 2116

Alfa AF: 0.0912 Hom.: 556

Bravo AF: 0.0938

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.48
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs62090893; hg19: chr18-73050334;