ENST00000738164.1:n.299+13497G>T

Variant names:

• chr10-10104269-G-T
• rs7088282
• ENST00000738164.1:n.299+13497G>T

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.299+13497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,112 control chromosomes in the GnomAD database, including 4,059 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 0.21 (4059 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 4 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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
ENSG00000296323	ENST00000738164.1	n.299+13497G>T		intron_variant	Intron 3 of 8
ENSG00000296323	ENST00000738165.1	n.326+13497G>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31566 AN: 151994 Hom.: 4055 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.208 AC: 31589 AN: 152112 Hom.: 4059 Cov.: 32 AF XY: 0.209 AC XY: 15517 AN XY: 74348

African (AFR) AF: 0.0942 AC: 3909 AN: 41514

American (AMR) AF: 0.181 AC: 2773 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1050 AN: 3472

East Asian (EAS) AF: 0.00696 AC: 36 AN: 5176

South Asian (SAS) AF: 0.160 AC: 772 AN: 4818

European-Finnish (FIN) AF: 0.361 AC: 3817 AN: 10570

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18459 AN: 67972

Other (OTH) AF: 0.190 AC: 401 AN: 2106

Alfa AF: 0.244 Hom.: 1244

Bravo AF: 0.187

Asia WGS AF: 0.0830 AC: 291 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	2.8
DANN	Benign	0.50
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs7088282; hg19: chr10-10146232;