rs12654265

Positions:

• 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 ENST00000663819.1(ENSG00000286749):​n.184-751T>C 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 0.276 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: ENST00000663819.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663819.1	n.184-751T>C		intron_variant, non_coding_transcript_variant
	ENST00000663460.1	n.217-751T>C		intron_variant, non_coding_transcript_variant

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;