rs2402446

Variant names:

• chr14-94399800-T-A
• rs2402446
• ENST00000693506.1:n.124+8906T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693506.1(ENSG00000289541):​n.124+8906T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,088 control chromosomes in the GnomAD database, including 31,826 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 0.63 (31826 hom., cov: 33)
• Consequence: ENSG00000289541 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

Genes affected

ENSG00000289541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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
ENSG00000289541	ENST00000693506.1	n.124+8906T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96351 AN: 151970 Hom.: 31785 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.634 AC: 96448 AN: 152088 Hom.: 31826 Cov.: 33 AF XY: 0.636 AC XY: 47249 AN XY: 74344

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.629

Alfa AF: 0.579 Hom.: 3285

Bravo AF: 0.638

Asia WGS AF: 0.643 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2402446; hg19: chr14-94866137;