chr20-714250-T-C

Variant names:

• chr20-714250-T-C
• rs1114734

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 0.12 in 152,234 control chromosomes in the GnomAD database, including 1,253 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 0.12 (1253 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.120 AC: 18245 AN: 152116 Hom.: 1241 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.120 AC: 18309 AN: 152234 Hom.: 1253 Cov.: 33 AF XY: 0.117 AC XY: 8745 AN XY: 74452

African (AFR) AF: 0.174 AC: 7225 AN: 41516

American (AMR) AF: 0.0851 AC: 1302 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3468

East Asian (EAS) AF: 0.161 AC: 836 AN: 5192

South Asian (SAS) AF: 0.109 AC: 526 AN: 4826

European-Finnish (FIN) AF: 0.0646 AC: 685 AN: 10608

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6814 AN: 68006

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.110 Hom.: 2063

Bravo AF: 0.124

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.66
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1114734; hg19: chr20-694894;