ENST00000663460.1:n.217-751T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663460.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286749	ENST00000663460.1		n.217-751T>C		intron	N/A
	ENSG00000286749	ENST00000663819.1		n.184-751T>C		intron	N/A
	ENSG00000286749	ENST00000812686.1		n.152-751T>C		intron	N/A

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

African (AFR) AF: 0.149 AC: 6184 AN: 41532

American (AMR) AF: 0.327 AC: 4993 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5180

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4826

European-Finnish (FIN) AF: 0.319 AC: 3374 AN: 10580

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23127 AN: 67972

Other (OTH) AF: 0.281 AC: 595 AN: 2116

Alfa AF: 0.229 Hom.: 807

Bravo AF: 0.272

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		0.25

Splicing

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

Other links and lift over

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