rs12654265

Variant names:

• chr5-152536953-T-C
• rs12654265
• ENST00000663460.1:n.217-751T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-152536953-T-C
• chr5-152536953-T-G

Variant summary

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

The ENST00000663460.1(ENSG00000286749):​n.217-751T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,138 control chromosomes in the GnomAD database, including 6,509 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 0.28 (6509 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000663460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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
ENSG00000286749	ENST00000663460.1	n.217-751T>C		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000663819.1	n.184-751T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41927 AN: 152020 Hom.: 6504 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.276 AC: 41945 AN: 152138 Hom.: 6509 Cov.: 32 AF XY: 0.274 AC XY: 20392 AN XY: 74362

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.281

Alfa AF: 0.232 Hom.: 792

Bravo AF: 0.272

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12654265; hg19: chr5-151916514; COSMIC: COSV60213998;