rs2318502

Variant names:

• chr14-19902007-C-A
• rs2318502

Your query was ambiguous. Multiple possible variants found:

• chr14-19902007-C-A
• chr14-19902007-C-T

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 0.347 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.192 AC: 7849 AN: 40906

American (AMR) AF: 0.373 AC: 5552 AN: 14868

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1447 AN: 3328

East Asian (EAS) AF: 0.177 AC: 896 AN: 5054

South Asian (SAS) AF: 0.349 AC: 1621 AN: 4640

European-Finnish (FIN) AF: 0.379 AC: 3886 AN: 10256

Middle Eastern (MID) AF: 0.372 AC: 105 AN: 282

European-Non Finnish (NFE) AF: 0.439 AC: 28952 AN: 65914

Other (OTH) AF: 0.374 AC: 764 AN: 2044

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
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs2318502; hg19: chr14-20370166;