18-67928681-T-C

Variant names:

• chr18-67928681-T-C
• rs726523

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 0.622 in 151,948 control chromosomes in the GnomAD database, including 31,577 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 0.62 (31577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 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: 0.623 AC: 94537 AN: 151830 Hom.: 31578 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.622 AC: 94541 AN: 151948 Hom.: 31577 Cov.: 32 AF XY: 0.625 AC XY: 46388 AN XY: 74264

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.636

Alfa AF: 0.717 Hom.: 38109

Bravo AF: 0.609

Asia WGS AF: 0.654 AC: 2251 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726523; hg19: chr18-65595918;