rs1522928

Variant names:

• chr2-73298409-C-T
• rs1522928
• ENST00000846694.1:n.174-157C>T

Variant summary

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

The ENST00000846694.1(ENSG00000310032):​n.174-157C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,052 control chromosomes in the GnomAD database, including 7,546 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 0.23 (7546 hom., cov: 32)
• Consequence: ENSG00000310032 ENST00000846694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 7 publications found

Genes affected

ENSG00000310032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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
ENSG00000310032	ENST00000846694.1	n.174-157C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34807 AN: 151934 Hom.: 7510 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.230 AC: 34906 AN: 152052 Hom.: 7546 Cov.: 32 AF XY: 0.230 AC XY: 17095 AN XY: 74358

African (AFR) AF: 0.557 AC: 23081 AN: 41442

American (AMR) AF: 0.206 AC: 3145 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2035 AN: 5166

South Asian (SAS) AF: 0.221 AC: 1068 AN: 4828

European-Finnish (FIN) AF: 0.0552 AC: 583 AN: 10554

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0589 AC: 4004 AN: 68000

Other (OTH) AF: 0.200 AC: 422 AN: 2106

Alfa AF: 0.112 Hom.: 3531

Bravo AF: 0.259

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.70
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1522928; hg19: chr2-73525537;