ENST00000650453.1:n.979-14509G>A

Variant names:

• chr9-84568688-G-A
• rs10512150
• ENST00000650453.1:n.979-14509G>A

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-14509G>A 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 152,240 control chromosomes in the GnomAD database, including 884 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 (884 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 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=-0.96).
• 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.600-14509G>A		intron_variant	Intron 4 of 13
LOC102724036	XR_007061622.1	n.3429+10634G>A		intron_variant	Intron 7 of 16
LOC102724036	XR_007061623.1	n.6210-5788G>A		intron_variant	Intron 7 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.979-14509G>A		intron_variant	Intron 3 of 6
ENSG00000285987	ENST00000728338.1	n.1045+10634G>A		intron_variant	Intron 5 of 6
ENSG00000285987	ENST00000728339.1	n.784-10083G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14911 AN: 152122 Hom.: 877 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: 0.0568

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0982 AC: 14950 AN: 152240 Hom.: 884 Cov.: 32 AF XY: 0.0988 AC XY: 7358 AN XY: 74452

African (AFR) AF: 0.166 AC: 6897 AN: 41526

American (AMR) AF: 0.127 AC: 1948 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5184

South Asian (SAS) AF: 0.0467 AC: 225 AN: 4818

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0605 AC: 4114 AN: 68010

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0870 Hom.: 94

Bravo AF: 0.107

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10512150; hg19: chr9-87183603;