2-45053565-A-G

Variant names:

• chr2-45053565-A-G
• rs17032957
• ENST00000716438.1:n.161+50933A>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+50933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 150,578 control chromosomes in the GnomAD database, including 6,494 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 0.28 (6494 hom., cov: 28)
• Consequence: ENSG00000286728 ENST00000716438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 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+50933A>G		intron_variant	Intron 2 of 2
ENSG00000286728	ENST00000716439.1	n.570+50933A>G		intron_variant	Intron 3 of 4
ENSG00000286728	ENST00000716440.1	n.136+50933A>G		intron_variant	Intron 2 of 5
ENSG00000286728	ENST00000716442.1	n.139-16456A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 42772 AN: 150462 Hom.: 6478 Cov.: 28

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.284 AC: 42839 AN: 150578 Hom.: 6494 Cov.: 28 AF XY: 0.292 AC XY: 21423 AN XY: 73424

African (AFR) AF: 0.242 AC: 9896 AN: 40818

American (AMR) AF: 0.376 AC: 5687 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1172 AN: 3462

East Asian (EAS) AF: 0.593 AC: 2962 AN: 4992

South Asian (SAS) AF: 0.433 AC: 2064 AN: 4766

European-Finnish (FIN) AF: 0.263 AC: 2705 AN: 10290

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17399 AN: 67838

Other (OTH) AF: 0.296 AC: 619 AN: 2092

Alfa AF: 0.275 Hom.: 7794

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.37
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs17032957; hg19: chr2-45280704;