rs1114734

Variant names:

• chr20-714250-T-C
• rs1114734

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0851

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0646

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.120

Alfa AF: 0.104 Hom.: 1190

Bravo AF: 0.124

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1114734; hg19: chr20-694894;