rs1587893

Variant names:

• chr18-78178925-T-C
• rs1587893

Your query was ambiguous. Multiple possible variants found:

• chr18-78178925-T-C
• chr18-78178925-T-G

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 0.75 in 152,172 control chromosomes in the GnomAD database, including 43,791 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 0.75 (43791 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.750 AC: 114053 AN: 152054 Hom.: 43740 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.750 AC: 114159 AN: 152172 Hom.: 43791 Cov.: 33 AF XY: 0.745 AC XY: 55446 AN XY: 74386

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.737

Alfa AF: 0.720 Hom.: 9857

Bravo AF: 0.758

Asia WGS AF: 0.660 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1587893; hg19: chr18-75938925;