rs2318502

chr14-19902007-C-Achr14-19902007-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 0.347 in 148,172 control chromosomes in the GnomAD database, including 6,141 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 0.35 (6141 hom., cov: 38)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.347 AC: 51423 AN: 148054 Hom.: 6143 Cov.: 38

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.347 AC: 51430 AN: 148172 Hom.: 6141 Cov.: 38 AF XY: 0.344 AC XY: 24874 AN XY: 72398

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.374

Alfa AF: 0.233 Hom.: 310

Asia WGS AF: 0.289 AC: 1007 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	0.13
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: rs2318502; hg19: chr14-20370166;