10-52789608-C-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816733.1. 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
	ENSG00000306279	ENST00000816733.1		n.505-590C>T		intron	N/A
	ENSG00000306279	ENST00000816734.1		n.382-590C>T		intron	N/A
	ENSG00000306279	ENST00000816735.1		n.98-590C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7899656;

hg19: chr10-54549368;