8-127663886-A-G

Position:

• chr8-127663886-A-G

Variant summary

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

The ENST00000652367.1(ENSG00000286010):​n.3995T>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 0.0926 in 152,196 control chromosomes in the GnomAD database, including 795 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 0.093 (795 hom., cov: 32)
• Consequence: ENSG00000286010 ENST00000652367.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

ENSG00000286010 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375754	XR_001746085.2	n.4920T>C		non_coding_transcript_exon_variant	3/3
LOC105375754	XR_001746086.2	n.3878T>C		non_coding_transcript_exon_variant	3/3
LOC105375754	XR_007061106.1	n.5012T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286010	ENST00000652367.1	n.3995T>C		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14090 AN: 152078 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0926 AC: 14090 AN: 152196 Hom.: 795 Cov.: 32 AF XY: 0.0968 AC XY: 7203 AN XY: 74412

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0722 Hom.: 432

Bravo AF: 0.0863

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.85
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4133274; hg19: chr8-128676131;