chr14-89760907-C-G

Variant names:

• chr14-89760907-C-G
• rs2093746
• ENST00000555070.1:n.170+192999G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555070.1(ENSG00000259053):​n.170+192999G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,738 control chromosomes in the GnomAD database, including 31,359 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 0.64 (31359 hom., cov: 30)
• Consequence: ENSG00000259053 ENST00000555070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 5 publications found

Genes affected

ENSG00000259053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555070.1. 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
	ENSG00000259053	ENST00000555070.1	TSL:3	n.170+192999G>C		intron	N/A
	ENSG00000258792	ENST00000819592.1		n.445+10566G>C		intron	N/A
	ENSG00000258792	ENST00000819593.1		n.113+10566G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97031 AN: 151620 Hom.: 31342 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.640 AC: 97099 AN: 151738 Hom.: 31359 Cov.: 30 AF XY: 0.640 AC XY: 47415 AN XY: 74114

African (AFR) AF: 0.568 AC: 23497 AN: 41356

American (AMR) AF: 0.720 AC: 10971 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2667 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2501 AN: 5132

South Asian (SAS) AF: 0.637 AC: 3056 AN: 4800

European-Finnish (FIN) AF: 0.658 AC: 6914 AN: 10512

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45354 AN: 67926

Other (OTH) AF: 0.654 AC: 1373 AN: 2098

Alfa AF: 0.653 Hom.: 4045

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.74
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2093746; hg19: chr14-90227251;