rs2627282

Variant names:

• chr8-2923434-G-A
• rs2627282
• ENST00000725259.1:n.1167-2331G>A

Variant summary

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

The ENST00000725259.1(ENSG00000253853):​n.1167-2331G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,124 control chromosomes in the GnomAD database, including 5,691 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 0.24 (5691 hom., cov: 33)
• Consequence: ENSG00000253853 ENST00000725259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 0 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.1167-77571G>A		intron_variant	Intron 6 of 11
LOC105377785	NR_168442.1	n.1698-2331G>A		intron_variant	Intron 9 of 14
LOC105377785	NR_168443.1	n.1172-85134G>A		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000725259.1	n.1167-2331G>A		intron_variant	Intron 6 of 7
ENSG00000253853	ENST00000667660.1	n.-134G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37124 AN: 152006 Hom.: 5693 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.244 AC: 37117 AN: 152124 Hom.: 5691 Cov.: 33 AF XY: 0.239 AC XY: 17805 AN XY: 74352

African (AFR) AF: 0.0845 AC: 3509 AN: 41526

American (AMR) AF: 0.236 AC: 3612 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3466

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5190

South Asian (SAS) AF: 0.105 AC: 507 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3696 AN: 10550

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23606 AN: 67980

Other (OTH) AF: 0.269 AC: 568 AN: 2108

Alfa AF: 0.287 Hom.: 2569

Bravo AF: 0.231

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2627282; hg19: chr8-2780956;