chr18-68648521-T-C

Variant names:

• chr18-68648521-T-C
• rs627419

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 0.758 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.562 AC: 23253 AN: 41402

American (AMR) AF: 0.783 AC: 11944 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3029 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4314 AN: 5158

South Asian (SAS) AF: 0.895 AC: 4316 AN: 4822

European-Finnish (FIN) AF: 0.879 AC: 9309 AN: 10592

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56342 AN: 67966

Other (OTH) AF: 0.786 AC: 1656 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs627419; hg19: chr18-66315758;