chr10-52811091-G-A

Variant names:

• chr10-52811091-G-A
• rs7917334
• ENST00000816733.1:n.692+394G>A

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,890 control chromosomes in the GnomAD database, including 22,305 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 0.53 (22305 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306279	ENST00000816733.1		n.692+394G>A		intron	N/A
	ENSG00000306279	ENST00000816737.1		n.124+394G>A		intron	N/A
	ENSG00000306301	ENST00000816878.1		n.-128C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79864 AN: 151772 Hom.: 22296 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.526 AC: 79887 AN: 151890 Hom.: 22305 Cov.: 31 AF XY: 0.524 AC XY: 38930 AN XY: 74244

African (AFR) AF: 0.353 AC: 14616 AN: 41404

American (AMR) AF: 0.433 AC: 6605 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3344 AN: 5152

South Asian (SAS) AF: 0.553 AC: 2664 AN: 4818

European-Finnish (FIN) AF: 0.644 AC: 6779 AN: 10532

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41865 AN: 67946

Other (OTH) AF: 0.540 AC: 1140 AN: 2110

Alfa AF: 0.580 Hom.: 41306

Bravo AF: 0.500

Asia WGS AF: 0.604 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.48
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7917334; hg19: chr10-54570851;