18-66649298-T-C

Position:

• chr18-66649298-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 0.308 in 151,904 control chromosomes in the GnomAD database, including 8,308 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 0.31 (8308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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: 0.308 AC: 46760 AN: 151786 Hom.: 8304 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.308 AC: 46786 AN: 151904 Hom.: 8308 Cov.: 32 AF XY: 0.314 AC XY: 23300 AN XY: 74228

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.336

Alfa AF: 0.356 Hom.: 9694

Bravo AF: 0.283

Asia WGS AF: 0.384 AC: 1336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs556372; hg19: chr18-64316535;