10-90987596-T-C

Variant names:

• chr10-90987596-T-C
• rs2027108
• ENST00000846062.1:n.152+25318A>G

Variant summary

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

The ENST00000846062.1(ENSG00000273124):​n.152+25318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,082 control chromosomes in the GnomAD database, including 26,394 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 0.59 (26394 hom., cov: 32)
• Consequence: ENSG00000273124 ENST00000846062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 publications found

Genes affected

ENSG00000273124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XLOC_008559	NR_131214.1	n.422+2051T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273124	ENST00000846062.1	n.152+25318A>G		intron_variant	Intron 2 of 2
ENSG00000273124	ENST00000846063.1	n.95-26333A>G		intron_variant	Intron 1 of 1
ENSG00000273124	ENST00000846064.1	n.270+25318A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89177 AN: 151964 Hom.: 26369 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.587 AC: 89250 AN: 152082 Hom.: 26394 Cov.: 32 AF XY: 0.592 AC XY: 44051 AN XY: 74354

African (AFR) AF: 0.578 AC: 23989 AN: 41484

American (AMR) AF: 0.557 AC: 8516 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1949 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4143 AN: 5168

South Asian (SAS) AF: 0.625 AC: 3009 AN: 4816

European-Finnish (FIN) AF: 0.631 AC: 6676 AN: 10572

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39237 AN: 67972

Other (OTH) AF: 0.542 AC: 1144 AN: 2110

Alfa AF: 0.574 Hom.: 4097

Bravo AF: 0.574

Asia WGS AF: 0.695 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2027108; hg19: chr10-92747353;