18-76736773-C-T

Variant names:

• chr18-76736773-C-T
• rs4891196

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 0.796 in 152,162 control chromosomes in the GnomAD database, including 48,325 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 0.80 (48325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121049 AN: 152044 Hom.: 48282 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.796 AC: 121153 AN: 152162 Hom.: 48325 Cov.: 32 AF XY: 0.796 AC XY: 59244 AN XY: 74404

African (AFR) AF: 0.794 AC: 32951 AN: 41500

American (AMR) AF: 0.755 AC: 11536 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3468

East Asian (EAS) AF: 0.770 AC: 3988 AN: 5176

South Asian (SAS) AF: 0.678 AC: 3269 AN: 4818

European-Finnish (FIN) AF: 0.841 AC: 8918 AN: 10600

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54994 AN: 67998

Other (OTH) AF: 0.806 AC: 1703 AN: 2114

Alfa AF: 0.802 Hom.: 98924

Bravo AF: 0.794

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.46
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4891196; hg19: chr18-74448729;