rs2369049

Variant names:

• chr14-95705514-A-G
• rs2369049

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 0.291 in 151,992 control chromosomes in the GnomAD database, including 10,994 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 0.29 (10994 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44119 AN: 151874 Hom.: 10956 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.291 AC: 44217 AN: 151992 Hom.: 10994 Cov.: 31 AF XY: 0.288 AC XY: 21430 AN XY: 74306

African (AFR) AF: 0.682 AC: 28270 AN: 41422

American (AMR) AF: 0.178 AC: 2711 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3466

East Asian (EAS) AF: 0.0907 AC: 470 AN: 5184

South Asian (SAS) AF: 0.189 AC: 909 AN: 4812

European-Finnish (FIN) AF: 0.203 AC: 2137 AN: 10540

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8510 AN: 67980

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.174 Hom.: 12100

Bravo AF: 0.303

Asia WGS AF: 0.195 AC: 676 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2369049; hg19: chr14-96171851;