chr14-89760907-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000259053	ENST00000555070.1	n.170+192999G>C		intron_variant	Intron 2 of 3	3

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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.654

Alfa AF: 0.653 Hom.: 4045

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2093746; hg19: chr14-90227251;