18-78299948-T-C

Variant names:

• chr18-78299948-T-C
• rs626549

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 0.813 in 151,638 control chromosomes in the GnomAD database, including 51,036 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 (51036 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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 (NFE) allele frequency at 95% confidence interval = 0.89 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: 0.813 AC: 123180 AN: 151520 Hom.: 51000 Cov.: 28

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.813 AC: 123268 AN: 151638 Hom.: 51036 Cov.: 28 AF XY: 0.816 AC XY: 60452 AN XY: 74092

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.824

Alfa AF: 0.854 Hom.: 14339

Bravo AF: 0.797

Asia WGS AF: 0.783 AC: 2728 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	0.022
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs626549; hg19: chr18-76059948;