chr2-45069386-A-G

Variant names:

• chr2-45069386-A-G
• rs868542
• ENST00000716438.1:n.161+66754A>G

Variant summary

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

The ENST00000716438.1(ENSG00000286728):​n.161+66754A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,046 control chromosomes in the GnomAD database, including 44,178 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 (44178 hom., cov: 31)
• Consequence: ENSG00000286728 ENST00000716438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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+66754A>G		intron_variant	Intron 2 of 2
ENSG00000286728	ENST00000716439.1	n.570+66754A>G		intron_variant	Intron 3 of 4
ENSG00000286728	ENST00000716440.1	n.136+66754A>G		intron_variant	Intron 2 of 5
ENSG00000286728	ENST00000716442.1	n.139-635A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115624 AN: 151928 Hom.: 44134 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.761 AC: 115730 AN: 152046 Hom.: 44178 Cov.: 31 AF XY: 0.759 AC XY: 56412 AN XY: 74290

African (AFR) AF: 0.814 AC: 33766 AN: 41492

American (AMR) AF: 0.766 AC: 11703 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3526 AN: 5144

South Asian (SAS) AF: 0.719 AC: 3466 AN: 4820

European-Finnish (FIN) AF: 0.724 AC: 7621 AN: 10532

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.746 AC: 50731 AN: 67982

Other (OTH) AF: 0.757 AC: 1600 AN: 2114

Alfa AF: 0.750 Hom.: 71723

Bravo AF: 0.764

Asia WGS AF: 0.704 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs868542; hg19: chr2-45296525;