18-29700738-C-T

Variant names:

• chr18-29700738-C-T
• rs10502528

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 0.159 in 151,984 control chromosomes in the GnomAD database, including 2,295 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 0.16 (2295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 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: 0.159 AC: 24129 AN: 151866 Hom.: 2289 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.159 AC: 24133 AN: 151984 Hom.: 2295 Cov.: 32 AF XY: 0.160 AC XY: 11912 AN XY: 74286

African (AFR) AF: 0.0712 AC: 2955 AN: 41492

American (AMR) AF: 0.137 AC: 2088 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3466

East Asian (EAS) AF: 0.0689 AC: 357 AN: 5178

South Asian (SAS) AF: 0.161 AC: 773 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2825 AN: 10552

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13923 AN: 67900

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.185 Hom.: 7166

Bravo AF: 0.144

Asia WGS AF: 0.104 AC: 360 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10502528; hg19: chr18-27280703;