ENST00000564048.2:n.136-10874A>T

Variant names:

• chr16-49319593-A-T
• rs2216263
• ENST00000564048.2:n.136-10874A>T

Variant summary

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

The ENST00000564048.2(ENSG00000279249):​n.136-10874A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,268 control chromosomes in the GnomAD database, including 38,225 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 0.69 (38225 hom., cov: 30)
• Consequence: ENSG00000279249 ENST00000564048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

ENSG00000279249 (HGNC:56730):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
ENSG00000279249	ENST00000564048.2	n.136-10874A>T		intron_variant	Intron 1 of 3	6
ENSG00000279249	ENST00000623424.2	n.197-10874A>T		intron_variant	Intron 1 of 4	6
ENSG00000279249	ENST00000643467.1	n.659-10874A>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.694 AC: 104881 AN: 151152 Hom.: 38168 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.694 AC: 104994 AN: 151268 Hom.: 38225 Cov.: 30 AF XY: 0.697 AC XY: 51500 AN XY: 73900

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.721

Alfa AF: 0.601 Hom.: 3446

Bravo AF: 0.727

Asia WGS AF: 0.873 AC: 3028 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2216263; hg19: chr16-49353504;