2-45045673-C-T

Variant names:

• chr2-45045673-C-T
• rs921119
• ENST00000716438.1:n.161+43041C>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+43041C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 146,914 control chromosomes in the GnomAD database, including 45,194 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 0.78 (45194 hom., cov: 23)
• Consequence: ENSG00000286728 ENST00000716438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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+43041C>T		intron_variant	Intron 2 of 2
ENSG00000286728	ENST00000716439.1	n.570+43041C>T		intron_variant	Intron 3 of 4
ENSG00000286728	ENST00000716440.1	n.136+43041C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.779 AC: 114464 AN: 146852 Hom.: 45160 Cov.: 23

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.740

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.780 AC: 114529 AN: 146914 Hom.: 45194 Cov.: 23 AF XY: 0.784 AC XY: 55871 AN XY: 71270

African (AFR) AF: 0.900 AC: 35709 AN: 39696

American (AMR) AF: 0.810 AC: 12027 AN: 14840

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2161 AN: 3450

East Asian (EAS) AF: 0.915 AC: 4637 AN: 5068

South Asian (SAS) AF: 0.868 AC: 3968 AN: 4572

European-Finnish (FIN) AF: 0.740 AC: 6624 AN: 8948

Middle Eastern (MID) AF: 0.734 AC: 210 AN: 286

European-Non Finnish (NFE) AF: 0.701 AC: 47058 AN: 67110

Other (OTH) AF: 0.773 AC: 1577 AN: 2040

Alfa AF: 0.753 Hom.: 7302

Bravo AF: 0.790

Asia WGS AF: 0.883 AC: 3059 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs921119; hg19: chr2-45272812;