rs2714384

Variant names:

• chr18-27722984-C-T
• rs2714384

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 0.14 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.271 AC: 11215 AN: 41460

American (AMR) AF: 0.0834 AC: 1276 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3472

East Asian (EAS) AF: 0.0909 AC: 471 AN: 5182

South Asian (SAS) AF: 0.0819 AC: 395 AN: 4824

European-Finnish (FIN) AF: 0.0787 AC: 834 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6532 AN: 68028

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.105 Hom.: 1698

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2714384; hg19: chr18-25302948;