rs7917334

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-52811091-G-A
• chr10-52811091-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378306	XR_945963.2	n.683+285G>A		intron_variant	Intron 3 of 3
LOC105378307	XR_001747451.2	n.-126C>T		upstream_gene_variant
LOC105378307	XR_945965.3	n.-126C>T		upstream_gene_variant
LOC105378307	XR_945966.3	n.-126C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306279	ENST00000816733.1	n.692+394G>A		intron_variant	Intron 3 of 3
ENSG00000306279	ENST00000816737.1	n.124+394G>A		intron_variant	Intron 1 of 2
ENSG00000306301	ENST00000816878.1	n.-128C>T		upstream_gene_variant
ENSG00000306301	ENST00000816880.1	n.-126C>T		upstream_gene_variant

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 v4.3

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;