chr10-52815236-G-C

Variant names:

• chr10-52815236-G-C
• rs6480975
• ENST00000816733.1:n.692+4539G>C

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+4539G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,172 control chromosomes in the GnomAD database, including 47,701 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 0.79 (47701 hom., cov: 33)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 10 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 = 0.856 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.692+4539G>C		intron_variant	Intron 3 of 3
ENSG00000306279	ENST00000816737.1	n.218+2762G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119866 AN: 152054 Hom.: 47684 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.788 AC: 119931 AN: 152172 Hom.: 47701 Cov.: 33 AF XY: 0.787 AC XY: 58526 AN XY: 74388

African (AFR) AF: 0.671 AC: 27842 AN: 41486

American (AMR) AF: 0.784 AC: 11979 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2765 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4535 AN: 5172

South Asian (SAS) AF: 0.765 AC: 3685 AN: 4818

European-Finnish (FIN) AF: 0.836 AC: 8859 AN: 10598

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57608 AN: 68020

Other (OTH) AF: 0.800 AC: 1692 AN: 2114

Alfa AF: 0.811 Hom.: 5929

Bravo AF: 0.779

Asia WGS AF: 0.824 AC: 2858 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.65
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6480975; hg19: chr10-54574996;