chr18-28463039-A-C

Position:

• chr18-28463039-A-C

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 0.539 in 152,032 control chromosomes in the GnomAD database, including 24,925 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 0.54 (24925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81855 AN: 151914 Hom.: 24912 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.539 AC: 81889 AN: 152032 Hom.: 24925 Cov.: 32 AF XY: 0.544 AC XY: 40417 AN XY: 74272

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.585

Alfa AF: 0.625 Hom.: 18196

Bravo AF: 0.530

Asia WGS AF: 0.683 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
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: rs12966353; hg19: chr18-26043003;