18-78096894-T-C

Position:

• chr18-78096894-T-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 0.631 in 152,108 control chromosomes in the GnomAD database, including 31,369 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 0.63 (31369 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.630 AC: 95809 AN: 151990 Hom.: 31298 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.631 AC: 95936 AN: 152108 Hom.: 31369 Cov.: 33 AF XY: 0.634 AC XY: 47155 AN XY: 74342

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.612

Alfa AF: 0.595 Hom.: 4305

Bravo AF: 0.627

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233747; hg19: chr18-75856894;