10-86402481-A-G

Position:

• chr10-86402481-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671245.1(ENSG00000286359):​n.296T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,194 control chromosomes in the GnomAD database, including 57,703 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 0.87 (57703 hom., cov: 32)
• Consequence: ENST00000671245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902473	XR_007062221.1	n.283T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671245.1	n.296T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132256 AN: 152076 Hom.: 57665 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.870 AC: 132349 AN: 152194 Hom.: 57703 Cov.: 32 AF XY: 0.873 AC XY: 64948 AN XY: 74410

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.826

Alfa AF: 0.865 Hom.: 52869

Bravo AF: 0.856

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10458771; hg19: chr10-88162238;