2-45053070-G-T

Variant names:

• chr2-45053070-G-T
• rs11894159
• ENST00000716438.1:n.161+50438G>T

Variant summary

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

The ENST00000716438.1(ENSG00000286728):​n.161+50438G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,064 control chromosomes in the GnomAD database, including 44,330 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 0.76 (44330 hom., cov: 31)
• Consequence: ENSG00000286728 ENST00000716438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 1 publications found

Genes affected

ENSG00000286728 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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
ENSG00000286728	ENST00000716438.1	n.161+50438G>T		intron_variant	Intron 2 of 2
ENSG00000286728	ENST00000716439.1	n.570+50438G>T		intron_variant	Intron 3 of 4
ENSG00000286728	ENST00000716440.1	n.136+50438G>T		intron_variant	Intron 2 of 5
ENSG00000286728	ENST00000716442.1	n.139-16951G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114861 AN: 151946 Hom.: 44270 Cov.: 31

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.756 AC: 114980 AN: 152064 Hom.: 44330 Cov.: 31 AF XY: 0.760 AC XY: 56526 AN XY: 74328

African (AFR) AF: 0.895 AC: 37161 AN: 41500

American (AMR) AF: 0.785 AC: 11994 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4807 AN: 5168

South Asian (SAS) AF: 0.842 AC: 4038 AN: 4798

European-Finnish (FIN) AF: 0.702 AC: 7428 AN: 10578

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45046 AN: 67950

Other (OTH) AF: 0.744 AC: 1571 AN: 2112

Alfa AF: 0.704 Hom.: 8140

Bravo AF: 0.767

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.63
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs11894159; hg19: chr2-45280209;