chr9-29363267-G-A

Variant names:

• chr9-29363267-G-A
• rs2150864
• ENST00000775037.1:n.255-58387C>T

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.255-58387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,922 control chromosomes in the GnomAD database, including 34,132 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 0.67 (34132 hom., cov: 31)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 5 publications found

Genes affected

ENSG00000300910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775037.1. 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
	ENSG00000300910	ENST00000775037.1		n.255-58387C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101210 AN: 151806 Hom.: 34081 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.667 AC: 101318 AN: 151922 Hom.: 34132 Cov.: 31 AF XY: 0.661 AC XY: 49050 AN XY: 74242

African (AFR) AF: 0.750 AC: 31096 AN: 41464

American (AMR) AF: 0.638 AC: 9719 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2039 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2078 AN: 5134

South Asian (SAS) AF: 0.512 AC: 2470 AN: 4820

European-Finnish (FIN) AF: 0.668 AC: 7046 AN: 10554

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44729 AN: 67924

Other (OTH) AF: 0.657 AC: 1382 AN: 2104

Alfa AF: 0.651 Hom.: 63332

Bravo AF: 0.670

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2150864; hg19: chr9-29363265;