18-78544708-C-T

Variant names:

• chr18-78544708-C-T
• rs1561389

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 0.592 in 151,886 control chromosomes in the GnomAD database, including 26,933 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 0.59 (26933 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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 (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.592 AC: 89896 AN: 151766 Hom.: 26900 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.592 AC: 89984 AN: 151886 Hom.: 26933 Cov.: 32 AF XY: 0.593 AC XY: 43971 AN XY: 74196

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.611

Alfa AF: 0.620 Hom.: 22801

Bravo AF: 0.594

Asia WGS AF: 0.680 AC: 2366 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	0.19
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561389; hg19: chr18-76304708;