rs2714384

chr18-27722984-C-T

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 0.14 in 152,184 control chromosomes in the GnomAD database, including 1,995 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 0.14 (1995 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21216 AN: 152066 Hom.: 1991 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21253 AN: 152184 Hom.: 1995 Cov.: 33 AF XY: 0.137 AC XY: 10195 AN XY: 74406

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.0819

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.123

Alfa AF: 0.100 Hom.: 1142

Bravo AF: 0.147

Asia WGS AF: 0.0990 AC: 345 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.19
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2714384; hg19: chr18-25302948;