chr2-6556956-C-T

Variant names:

• chr2-6556956-C-T
• rs962528
• ENST00000790472.1:n.-125C>T

Variant summary

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

The ENST00000790472.1(ENSG00000302919):​n.-125C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,824 control chromosomes in the GnomAD database, including 6,139 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 0.26 (6139 hom., cov: 31)
• Consequence: ENSG00000302919 ENST00000790472.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 3 publications found

Genes affected

ENSG00000302919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 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
ENSG00000302919	ENST00000790472.1	n.-125C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40048 AN: 151706 Hom.: 6133 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.264 AC: 40063 AN: 151824 Hom.: 6139 Cov.: 31 AF XY: 0.268 AC XY: 19898 AN XY: 74196

African (AFR) AF: 0.101 AC: 4204 AN: 41428

American (AMR) AF: 0.291 AC: 4427 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1095 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2235 AN: 5126

South Asian (SAS) AF: 0.372 AC: 1793 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3845 AN: 10528

Middle Eastern (MID) AF: 0.245 AC: 71 AN: 290

European-Non Finnish (NFE) AF: 0.317 AC: 21514 AN: 67918

Other (OTH) AF: 0.265 AC: 559 AN: 2106

Alfa AF: 0.297 Hom.: 17574

Bravo AF: 0.248

Asia WGS AF: 0.407 AC: 1413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs962528; hg19: chr2-6697088;