10-87597759-T-C

Variant names:

• chr10-87597759-T-C
• rs1886280
• ENST00000446794.1:n.32-6016A>G

Variant summary

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

The ENST00000446794.1(ENSG00000223761):​n.32-6016A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,058 control chromosomes in the GnomAD database, including 41,427 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 0.73 (41427 hom., cov: 31)
• Consequence: ENSG00000223761 ENST00000446794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 3 publications found

Genes affected

ENSG00000223761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378412	XR_946171.2	n.86+1225T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223761	ENST00000446794.1	n.32-6016A>G		intron_variant	Intron 1 of 1	3
ENSG00000225913	ENST00000804457.1	n.103-8542T>C		intron_variant	Intron 1 of 4
ENSG00000225913	ENST00000804458.1	n.113+1225T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110423 AN: 151940 Hom.: 41365 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.727 AC: 110548 AN: 152058 Hom.: 41427 Cov.: 31 AF XY: 0.728 AC XY: 54114 AN XY: 74290

African (AFR) AF: 0.922 AC: 38293 AN: 41514

American (AMR) AF: 0.709 AC: 10831 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2410 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3769 AN: 5162

South Asian (SAS) AF: 0.750 AC: 3608 AN: 4812

European-Finnish (FIN) AF: 0.656 AC: 6916 AN: 10548

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

European-Non Finnish (NFE) AF: 0.625 AC: 42471 AN: 67974

Other (OTH) AF: 0.718 AC: 1513 AN: 2108

Alfa AF: 0.671 Hom.: 68266

Bravo AF: 0.734

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1886280; hg19: chr10-89357516;