10-88063390-A-G

Variant names:

• chr10-88063390-A-G
• rs945559
• ENST00000752267.1:n.648+1960A>G

Variant summary

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

The ENST00000752267.1(ENSG00000297977):​n.648+1960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,032 control chromosomes in the GnomAD database, including 18,650 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 0.47 (18650 hom., cov: 32)
• Consequence: ENSG00000297977 ENST00000752267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 2 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752267.1. 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
	ENSG00000297977	ENST00000752267.1		n.648+1960A>G		intron	N/A
	ENSG00000297977	ENST00000752268.1		n.586+1960A>G		intron	N/A
	ENSG00000288875	ENST00000752393.1		n.260-13799T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71244 AN: 151914 Hom.: 18647 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.469 AC: 71256 AN: 152032 Hom.: 18650 Cov.: 32 AF XY: 0.471 AC XY: 35000 AN XY: 74336

African (AFR) AF: 0.229 AC: 9501 AN: 41470

American (AMR) AF: 0.549 AC: 8391 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3962 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5653 AN: 10564

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38345 AN: 67932

Other (OTH) AF: 0.482 AC: 1019 AN: 2112

Alfa AF: 0.526 Hom.: 22177

Bravo AF: 0.463

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.71
DANN	Benign	0.57
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs945559; hg19: chr10-89823147;