ENST00000816733.1:n.692+15591T>C

Variant names:

• chr10-52826288-T-C
• rs4098805
• ENST00000816733.1:n.692+15591T>C

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+15591T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,862 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 5 publications found

Genes affected

ENSG00000306279 (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 (AMR) allele frequency at 95% confidence interval = 0.326 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
ENSG00000306279	ENST00000816733.1	n.692+15591T>C		intron_variant	Intron 3 of 3
ENSG00000306279	ENST00000816737.1	n.219-757T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37005 AN: 151746 Hom.: 4637 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37029 AN: 151862 Hom.: 4645 Cov.: 31 AF XY: 0.244 AC XY: 18090 AN XY: 74210

African (AFR) AF: 0.239 AC: 9901 AN: 41426

American (AMR) AF: 0.334 AC: 5076 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1531 AN: 5132

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15929 AN: 67920

Other (OTH) AF: 0.249 AC: 524 AN: 2106

Alfa AF: 0.242 Hom.: 15197

Bravo AF: 0.256

Asia WGS AF: 0.247 AC: 860 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	1.1
DANN	Benign	0.69
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4098805; hg19: chr10-54586048;