ENST00000664527.1:n.490+603A>G

Variant names:

• chr12-49537802-T-C
• rs11169063
• ENST00000664527.1:n.490+603A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664527.1(ENSG00000287537):​n.490+603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,972 control chromosomes in the GnomAD database, including 12,454 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 0.34 (12454 hom., cov: 31)
• Consequence: ENSG00000287537 ENST00000664527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.30
• Publications: 5 publications found

Genes affected

ENSG00000287537 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287537	ENST00000664527.1		n.490+603A>G		intron	N/A
	ENSG00000287537	ENST00000815353.1		n.373+603A>G		intron	N/A
	ENSG00000287537	ENST00000815354.1		n.303+603A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51909 AN: 151854 Hom.: 12398 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0814

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.342 AC: 52020 AN: 151972 Hom.: 12454 Cov.: 31 AF XY: 0.340 AC XY: 25242 AN XY: 74270

African (AFR) AF: 0.684 AC: 28361 AN: 41456

American (AMR) AF: 0.223 AC: 3404 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3466

East Asian (EAS) AF: 0.0812 AC: 419 AN: 5160

South Asian (SAS) AF: 0.204 AC: 978 AN: 4798

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10540

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14219 AN: 67958

Other (OTH) AF: 0.303 AC: 640 AN: 2110

Alfa AF: 0.232 Hom.: 10847

Bravo AF: 0.351

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.028
DANN	Benign	0.52
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs11169063; hg19: chr12-49931585;