9-84650211-C-T

Variant names:

• chr9-84650211-C-T
• rs10868223
• ENST00000650453.1:n.1342-5003C>T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.1342-5003C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 142,666 control chromosomes in the GnomAD database, including 1,162 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 0.12 (1162 hom., cov: 28)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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.1342-5003C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 16555 AN: 142590 Hom.: 1155 Cov.: 28

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.116 AC: 16578 AN: 142666 Hom.: 1162 Cov.: 28 AF XY: 0.120 AC XY: 8229 AN XY: 68646

African (AFR) AF: 0.0605 AC: 2272 AN: 37540

American (AMR) AF: 0.175 AC: 2446 AN: 14006

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 628 AN: 3448

East Asian (EAS) AF: 0.267 AC: 1306 AN: 4886

South Asian (SAS) AF: 0.221 AC: 1005 AN: 4538

European-Finnish (FIN) AF: 0.0599 AC: 501 AN: 8368

Middle Eastern (MID) AF: 0.248 AC: 65 AN: 262

European-Non Finnish (NFE) AF: 0.119 AC: 7916 AN: 66770

Other (OTH) AF: 0.161 AC: 313 AN: 1948

Alfa AF: 0.102 Hom.: 119

Bravo AF: 0.118

Asia WGS AF: 0.270 AC: 937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10868223; hg19: chr9-87265126;