chr18-67284976-C-T

Position:

• chr18-67284976-C-T

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 0.408 in 151,890 control chromosomes in the GnomAD database, including 13,357 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 0.41 (13357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.408 AC: 61925 AN: 151768 Hom.: 13347 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.408 AC: 61975 AN: 151890 Hom.: 13357 Cov.: 32 AF XY: 0.415 AC XY: 30792 AN XY: 74222

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.403

Alfa AF: 0.371 Hom.: 21177

Bravo AF: 0.406

Asia WGS AF: 0.670 AC: 2319 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8099213; hg19: chr18-64952213;