18-78078302-T-C

Variant names:

• chr18-78078302-T-C
• rs4798954

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 0.531 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.212 AC: 8775 AN: 41484

American (AMR) AF: 0.622 AC: 9493 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2395 AN: 5162

South Asian (SAS) AF: 0.550 AC: 2645 AN: 4806

European-Finnish (FIN) AF: 0.597 AC: 6303 AN: 10558

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46906 AN: 67992

Other (OTH) AF: 0.554 AC: 1165 AN: 2104

Alfa AF: 0.633 Hom.: 96005

Bravo AF: 0.520

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.022
DANN	Benign	0.23
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4798954; hg19: chr18-75838302;