18-71696509-C-T

Variant names:

• chr18-71696509-C-T
• rs4374282

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 0.202 in 152,044 control chromosomes in the GnomAD database, including 3,762 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 0.20 (3762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30654 AN: 151926 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.202 AC: 30661 AN: 152044 Hom.: 3762 Cov.: 32 AF XY: 0.206 AC XY: 15276 AN XY: 74278

African (AFR) AF: 0.0672 AC: 2791 AN: 41520

American (AMR) AF: 0.211 AC: 3217 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 563 AN: 3462

East Asian (EAS) AF: 0.297 AC: 1525 AN: 5140

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3373 AN: 10556

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17328 AN: 67960

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.220 Hom.: 4673

Bravo AF: 0.189

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs4374282; hg19: chr18-69363745;