ENST00000787527.1:n.96-681A>G

Variant names:

• chr2-184188055-T-C
• rs10497643
• ENST00000787527.1:n.96-681A>G

Variant summary

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

The ENST00000787527.1(ENSG00000286152):​n.96-681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,980 control chromosomes in the GnomAD database, including 16,215 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 0.42 (16215 hom., cov: 32)
• Consequence: ENSG00000286152 ENST00000787527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 3 publications found

Genes affected

ENSG00000286152 (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 (AMR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373777	XR_923654.2	n.26-681A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286152	ENST00000787527.1	n.96-681A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63888 AN: 151864 Hom.: 16211 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.420 AC: 63892 AN: 151980 Hom.: 16215 Cov.: 32 AF XY: 0.420 AC XY: 31172 AN XY: 74242

African (AFR) AF: 0.120 AC: 4985 AN: 41490

American (AMR) AF: 0.545 AC: 8328 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2413 AN: 5152

South Asian (SAS) AF: 0.484 AC: 2330 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10540

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36836 AN: 67932

Other (OTH) AF: 0.446 AC: 941 AN: 2110

Alfa AF: 0.393 Hom.: 2013

Bravo AF: 0.411

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.71
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs10497643; hg19: chr2-185052782;