10-16821162-G-A

Variant names:

• chr10-16821162-G-A
• rs780633
• ENST00000655281.2:n.513G>A

Variant summary

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

The ENST00000655281.2(ENSG00000286958):​n.513G>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 0.591 in 152,080 control chromosomes in the GnomAD database, including 28,326 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 (28326 hom., cov: 33)
• Consequence: ENSG00000286958 ENST00000655281.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 14 publications found

Genes affected

ENSG00000286958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655281.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286958	ENST00000655281.2		n.513G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286958	ENST00000806588.1		n.510G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286958	ENST00000806589.1		n.446G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89736 AN: 151962 Hom.: 28266 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.591 AC: 89858 AN: 152080 Hom.: 28326 Cov.: 33 AF XY: 0.594 AC XY: 44149 AN XY: 74322

African (AFR) AF: 0.818 AC: 33915 AN: 41484

American (AMR) AF: 0.586 AC: 8963 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4025 AN: 5174

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4828

European-Finnish (FIN) AF: 0.551 AC: 5809 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31484 AN: 67966

Other (OTH) AF: 0.539 AC: 1140 AN: 2116

Alfa AF: 0.522 Hom.: 16520

Bravo AF: 0.606

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.37
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs780633; hg19: chr10-16863161;