rs2896268

Variant names:

• chr14-94399371-A-C
• rs2896268
• ENST00000693506.1:n.124+8477A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-94399371-A-C
• chr14-94399371-A-G
• chr14-94399371-A-T

Variant summary

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

The ENST00000693506.1(ENSG00000289541):​n.124+8477A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,070 control chromosomes in the GnomAD database, including 23,909 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 0.55 (23909 hom., cov: 33)
• Consequence: ENSG00000289541 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

Genes affected

ENSG00000289541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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+8477A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83384 AN: 151952 Hom.: 23886 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.549 AC: 83456 AN: 152070 Hom.: 23909 Cov.: 33 AF XY: 0.546 AC XY: 40574 AN XY: 74336

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.546

Alfa AF: 0.496 Hom.: 3317

Bravo AF: 0.545

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2896268; hg19: chr14-94865708;