ENST00000816733.1:n.505-590C>T

Variant names:

• chr10-52789608-C-T
• rs7899656
• ENST00000816733.1:n.505-590C>T

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.505-590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,850 control chromosomes in the GnomAD database, including 4,074 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 0.22 (4074 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378306	XR_945963.2	n.387-590C>T		intron_variant	Intron 1 of 3
LOC105378307	XR_945965.3	n.370-5274G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306279	ENST00000816733.1	n.505-590C>T		intron_variant	Intron 1 of 3
ENSG00000306279	ENST00000816734.1	n.382-590C>T		intron_variant	Intron 1 of 2
ENSG00000306279	ENST00000816735.1	n.98-590C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33880 AN: 151732 Hom.: 4077 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.223 AC: 33872 AN: 151850 Hom.: 4074 Cov.: 31 AF XY: 0.220 AC XY: 16331 AN XY: 74224

African (AFR) AF: 0.151 AC: 6254 AN: 41294

American (AMR) AF: 0.182 AC: 2781 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3466

East Asian (EAS) AF: 0.140 AC: 724 AN: 5172

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4818

European-Finnish (FIN) AF: 0.231 AC: 2446 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18820 AN: 67958

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.257 Hom.: 4290

Bravo AF: 0.212

Asia WGS AF: 0.179 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.84
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7899656; hg19: chr10-54549368;