rs1893662

Variant names:

• chr18-38562923-G-A
• rs1893662

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 0.666 in 152,048 control chromosomes in the GnomAD database, including 36,082 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 0.67 (36082 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 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: 0.666 AC: 101223 AN: 151930 Hom.: 36086 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.666 AC: 101239 AN: 152048 Hom.: 36082 Cov.: 33 AF XY: 0.669 AC XY: 49757 AN XY: 74336

African (AFR) AF: 0.393 AC: 16274 AN: 41434

American (AMR) AF: 0.674 AC: 10302 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2628 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3314 AN: 5160

South Asian (SAS) AF: 0.729 AC: 3519 AN: 4824

European-Finnish (FIN) AF: 0.826 AC: 8746 AN: 10594

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54203 AN: 67980

Other (OTH) AF: 0.664 AC: 1399 AN: 2106

Alfa AF: 0.754 Hom.: 167498

Bravo AF: 0.642

Asia WGS AF: 0.649 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1893662; hg19: chr18-36142887;