chr18-68648521-T-C

Position:

• chr18-68648521-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 0.758 in 151,976 control chromosomes in the GnomAD database, including 44,898 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 0.76 (44898 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68648521T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115185 AN: 151858 Hom.: 44893 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.758 AC: 115211 AN: 151976 Hom.: 44898 Cov.: 31 AF XY: 0.765 AC XY: 56830 AN XY: 74298

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.786

Alfa AF: 0.783 Hom.: 7998

Bravo AF: 0.740

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs627419; hg19: chr18-66315758;