rs10512149

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285987	ENST00000650453.1		n.979-18550A>G		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.1045+6593A>G		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.784-14124A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10512149;

hg19: chr9-87179562;