rs2896268

chr14-94399371-A-Cchr14-94399371-A-Gchr14-94399371-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, non coding transcript 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: ENST00000693506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000693506.1	n.124+8477A>C		intron_variant, non_coding_transcript_variant

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;