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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693506.1(ENSG00000256357):​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: ENSG00000256357 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 11 publications found

Genes affected

ENSG00000256357 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693506.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256357	ENST00000693506.1		n.124+8477A>C		intron	N/A
	ENSG00000256357	ENST00000811346.1		n.227+9506A>C		intron	N/A
	ENSG00000256357	ENST00000811347.1		n.208+9506A>C		intron	N/A

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

African (AFR) AF: 0.711 AC: 29483 AN: 41480

American (AMR) AF: 0.377 AC: 5762 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1907 AN: 3472

East Asian (EAS) AF: 0.593 AC: 3066 AN: 5166

South Asian (SAS) AF: 0.585 AC: 2829 AN: 4832

European-Finnish (FIN) AF: 0.497 AC: 5245 AN: 10554

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33432 AN: 67968

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2896268; hg19: chr14-94865708;