18-78544708-C-T

Variant names:

• chr18-78544708-C-T
• rs1561389

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 0.592 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.500 AC: 20689 AN: 41376

American (AMR) AF: 0.632 AC: 9655 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2188 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3479 AN: 5154

South Asian (SAS) AF: 0.642 AC: 3094 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6311 AN: 10526

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42477 AN: 67950

Other (OTH) AF: 0.611 AC: 1288 AN: 2108

Alfa AF: 0.618 Hom.: 32874

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1561389; hg19: chr18-76304708;