ENST00000650453.1:n.979-18550A>G

Variant names:

• chr9-84564647-A-G
• rs10512149
• ENST00000650453.1:n.979-18550A>G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-18550A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,128 control chromosomes in the GnomAD database, including 883 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 0.098 (883 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 8 publications found

Genes affected

ENSG00000285987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724036	XR_001746805.1	n.600-18550A>G		intron_variant	Intron 4 of 13
LOC102724036	XR_007061622.1	n.3429+6593A>G		intron_variant	Intron 7 of 16
LOC102724036	XR_007061623.1	n.6209+6593A>G		intron_variant	Intron 7 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.979-18550A>G		intron_variant	Intron 3 of 6
ENSG00000285987	ENST00000728338.1	n.1045+6593A>G		intron_variant	Intron 5 of 6
ENSG00000285987	ENST00000728339.1	n.784-14124A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14898 AN: 152010 Hom.: 876 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0982 AC: 14937 AN: 152128 Hom.: 883 Cov.: 32 AF XY: 0.0988 AC XY: 7345 AN XY: 74370

African (AFR) AF: 0.166 AC: 6894 AN: 41498

American (AMR) AF: 0.127 AC: 1942 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3472

East Asian (EAS) AF: 0.0567 AC: 293 AN: 5172

South Asian (SAS) AF: 0.0476 AC: 229 AN: 4814

European-Finnish (FIN) AF: 0.0872 AC: 924 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4106 AN: 67978

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0726 Hom.: 327

Bravo AF: 0.107

Asia WGS AF: 0.0670 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.3
DANN	Benign	0.60
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10512149; hg19: chr9-87179562;