rs11169063

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287537 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287537	ENST00000664527.1	n.490+603A>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0812

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.303

Alfa AF: 0.219 Hom.: 6090

Bravo AF: 0.351

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11169063; hg19: chr12-49931585;