rs7902899

Variant names:

• chr10-52850672-G-A
• rs7902899
• ENST00000816733.1:n.693-6068G>A

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.693-6068G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,034 control chromosomes in the GnomAD database, including 17,920 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 0.46 (17920 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 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.693-6068G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69422 AN: 151916 Hom.: 17915 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.457 AC: 69435 AN: 152034 Hom.: 17920 Cov.: 32 AF XY: 0.457 AC XY: 33953 AN XY: 74328

African (AFR) AF: 0.217 AC: 9020 AN: 41474

American (AMR) AF: 0.387 AC: 5905 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2752 AN: 5154

South Asian (SAS) AF: 0.538 AC: 2593 AN: 4820

European-Finnish (FIN) AF: 0.610 AC: 6437 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.574 AC: 39011 AN: 67988

Other (OTH) AF: 0.474 AC: 1001 AN: 2112

Alfa AF: 0.492 Hom.: 2546

Bravo AF: 0.428

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7902899; hg19: chr10-54610432;