rs12522916

Positions:

• chr5-135911101-G-A

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, non coding transcript 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: ENST00000523722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000523722.1	n.240-1279C>T		intron_variant, non_coding_transcript_variant		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;