10-8083856-G-A

Variant names:

• chr10-8083856-G-A
• rs379568
• ENST00000826149.1:n.187G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000826149.1(ENSG00000307416):​n.187G>A 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 0.177 in 152,246 control chromosomes in the GnomAD database, including 3,295 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 0.18 (3295 hom., cov: 33)
• Consequence: ENSG00000307416 ENST00000826149.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59
• Publications: 5 publications found

Genes affected

ENSG00000307416 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826149.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307416	ENST00000826149.1		n.187G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307416	ENST00000826150.1		n.226G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26854 AN: 152128 Hom.: 3273 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.177 AC: 26918 AN: 152246 Hom.: 3295 Cov.: 33 AF XY: 0.176 AC XY: 13072 AN XY: 74438

African (AFR) AF: 0.355 AC: 14717 AN: 41514

American (AMR) AF: 0.150 AC: 2292 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.112 AC: 582 AN: 5178

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4828

European-Finnish (FIN) AF: 0.111 AC: 1182 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6883 AN: 68026

Other (OTH) AF: 0.160 AC: 338 AN: 2114

Alfa AF: 0.130 Hom.: 5657

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	21
DANN	Benign	0.78
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs379568; hg19: chr10-8125819;