rs2979684

Variant names:

• chr8-24959927-G-A
• rs2979684
• ENST00000814723.1:n.283G>A

Variant summary

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

The ENST00000814723.1(ENSG00000253832):​n.283G>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 0.546 in 151,846 control chromosomes in the GnomAD database, including 24,373 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 0.55 (24373 hom., cov: 31)
• Consequence: ENSG00000253832 ENST00000814723.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 5 publications found

Genes affected

ENSG00000253832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253832	ENST00000814723.1	n.283G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82861 AN: 151728 Hom.: 24363 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.546 AC: 82898 AN: 151846 Hom.: 24373 Cov.: 31 AF XY: 0.550 AC XY: 40814 AN XY: 74230

African (AFR) AF: 0.313 AC: 12974 AN: 41438

American (AMR) AF: 0.664 AC: 10122 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3470

East Asian (EAS) AF: 0.583 AC: 2994 AN: 5132

South Asian (SAS) AF: 0.671 AC: 3227 AN: 4806

European-Finnish (FIN) AF: 0.610 AC: 6424 AN: 10526

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43476 AN: 67930

Other (OTH) AF: 0.547 AC: 1145 AN: 2094

Alfa AF: 0.598 Hom.: 11099

Bravo AF: 0.540

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2979684; hg19: chr8-24817441;