18-78272137-C-T

Variant names:

• chr18-78272137-C-T
• rs1944016

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 0.807 in 152,062 control chromosomes in the GnomAD database, including 49,948 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 0.81 (49948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 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: 0.808 AC: 122706 AN: 151944 Hom.: 49915 Cov.: 31

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.807 AC: 122782 AN: 152062 Hom.: 49948 Cov.: 31 AF XY: 0.797 AC XY: 59285 AN XY: 74340

African (AFR) AF: 0.802 AC: 33239 AN: 41464

American (AMR) AF: 0.771 AC: 11782 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3032 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2905 AN: 5160

South Asian (SAS) AF: 0.717 AC: 3455 AN: 4816

European-Finnish (FIN) AF: 0.717 AC: 7566 AN: 10556

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58011 AN: 68006

Other (OTH) AF: 0.805 AC: 1701 AN: 2112

Alfa AF: 0.829 Hom.: 6772

Bravo AF: 0.811

Asia WGS AF: 0.667 AC: 2322 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	0.081
DANN	Benign	0.52
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1944016; hg19: chr18-76032137;