14-94600881-C-T

Variant names:

• chr14-94600881-C-T
• rs10145747
• ENST00000553947.1:n.*667+2670C>T

Variant summary

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

The ENST00000553947.1(ENSG00000273259):​n.*667+2670C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,050 control chromosomes in the GnomAD database, including 1,121 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 0.094 (1121 hom., cov: 32)
• Consequence: ENSG00000273259 ENST00000553947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 publications found

Genes affected

ENSG00000273259 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553947.1. 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
	ENSG00000273259	ENST00000553947.1	TSL:2	n.*667+2670C>T		intron	N/A	ENSP00000452367.2	G3V5I3
	ENSG00000288028	ENST00000656621.1		n.70+1352C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14274 AN: 151932 Hom.: 1120 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0954

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.0941 AC: 14302 AN: 152050 Hom.: 1121 Cov.: 32 AF XY: 0.0921 AC XY: 6847 AN XY: 74338

African (AFR) AF: 0.210 AC: 8704 AN: 41418

American (AMR) AF: 0.0535 AC: 818 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.0954 AC: 492 AN: 5156

South Asian (SAS) AF: 0.0856 AC: 413 AN: 4822

European-Finnish (FIN) AF: 0.0541 AC: 573 AN: 10584

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0440 AC: 2993 AN: 68006

Other (OTH) AF: 0.0887 AC: 187 AN: 2108

Alfa AF: 0.0629 Hom.: 803

Bravo AF: 0.0991

Asia WGS AF: 0.113 AC: 394 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs10145747; hg19: chr14-95067218;