rs12522916

Variant names:

• chr5-135911101-G-A
• rs12522916
• ENST00000523722.1:n.240-1279C>T

Variant summary

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

The ENST00000523722.1(ENSG00000253927):​n.240-1279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,180 control chromosomes in the GnomAD database, including 2,670 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 0.18 (2670 hom., cov: 32)
• Consequence: ENSG00000253927 ENST00000523722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

ENSG00000253927 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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
ENSG00000253927	ENST00000523722.1	n.240-1279C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27448 AN: 152062 Hom.: 2666 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.180 AC: 27455 AN: 152180 Hom.: 2670 Cov.: 32 AF XY: 0.181 AC XY: 13428 AN XY: 74384

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.198

Alfa AF: 0.207 Hom.: 1784

Bravo AF: 0.178

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12522916; hg19: chr5-135246790;