rs2369049

Variant names:

• chr14-95705514-A-G
• rs2369049

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 0.291 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.290 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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.234

Alfa AF: 0.141 Hom.: 4489

Bravo AF: 0.303

Asia WGS AF: 0.195 AC: 676 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2369049; hg19: chr14-96171851;