rs780633

Positions:

• chr10-16821162-G-A

Variant summary

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

The ENST00000655281.1(ENSG00000286958):​n.455G>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 ENST00000655281.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

ENSG00000286958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376435	XR_930708.3	n.455G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286958	ENST00000655281.1	n.455G>A		non_coding_transcript_exon_variant	3/3

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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.539

Alfa AF: 0.516 Hom.: 11406

Bravo AF: 0.606

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780633; hg19: chr10-16863161;