rs1893662

Variant names:

• chr18-38562923-G-A
• rs1893662

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.666 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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.664

Alfa AF: 0.772 Hom.: 71080

Bravo AF: 0.642

Asia WGS AF: 0.649 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893662; hg19: chr18-36142887;