ENST00000754095.1:n.99+23200C>T

Variant names:

• chr9-25551359-C-T
• rs17774966
• ENST00000754095.1:n.99+23200C>T

Variant summary

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

The ENST00000754095.1(ENSG00000298250):​n.99+23200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,710 control chromosomes in the GnomAD database, including 1,750 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 0.13 (1750 hom., cov: 32)
• Consequence: ENSG00000298250 ENST00000754095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 10 publications found

Genes affected

ENSG00000298250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375996	XR_929525.3	n.50-787G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298250	ENST00000754095.1	n.99+23200C>T		intron_variant	Intron 1 of 2
ENSG00000298267	ENST00000754302.1	n.49-9339G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19916 AN: 151592 Hom.: 1749 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.131 AC: 19913 AN: 151710 Hom.: 1750 Cov.: 32 AF XY: 0.127 AC XY: 9451 AN XY: 74158

African (AFR) AF: 0.0390 AC: 1617 AN: 41458

American (AMR) AF: 0.134 AC: 2033 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3464

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5166

South Asian (SAS) AF: 0.0764 AC: 368 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1705 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12767 AN: 67726

Other (OTH) AF: 0.153 AC: 322 AN: 2104

Alfa AF: 0.162 Hom.: 5586

Bravo AF: 0.125

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.77
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs17774966; hg19: chr9-25551357;