18-78078302-T-C

Variant names:

• chr18-78078302-T-C
• rs4798954

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 0.531 in 152,042 control chromosomes in the GnomAD database, including 24,663 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 0.53 (24663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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: 0.531 AC: 80651 AN: 151924 Hom.: 24642 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.531 AC: 80699 AN: 152042 Hom.: 24663 Cov.: 32 AF XY: 0.528 AC XY: 39223 AN XY: 74300

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.554

Alfa AF: 0.664 Hom.: 65260

Bravo AF: 0.520

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.022
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798954; hg19: chr18-75838302;