9-85399960-G-A

Variant names:

• chr9-85399960-G-A
• rs2841453
• ENST00000648131.1:n.600+1725C>T

Variant summary

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

The ENST00000648131.1(ENSG00000285634):​n.600+1725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,030 control chromosomes in the GnomAD database, including 36,010 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 0.68 (36010 hom., cov: 32)
• Consequence: ENSG00000285634 ENST00000648131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 2 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285634	ENST00000648131.1		n.600+1725C>T		intron	N/A
	ENSG00000285634	ENST00000662737.1		n.1680+1495C>T		intron	N/A
	ENSG00000285634	ENST00000669133.1		n.282+2587C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102876 AN: 151912 Hom.: 36008 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.677 AC: 102920 AN: 152030 Hom.: 36010 Cov.: 32 AF XY: 0.677 AC XY: 50264 AN XY: 74292

African (AFR) AF: 0.498 AC: 20620 AN: 41438

American (AMR) AF: 0.630 AC: 9636 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4296 AN: 5158

South Asian (SAS) AF: 0.670 AC: 3221 AN: 4810

European-Finnish (FIN) AF: 0.788 AC: 8335 AN: 10574

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51875 AN: 67988

Other (OTH) AF: 0.712 AC: 1495 AN: 2100

Alfa AF: 0.723 Hom.: 15432

Bravo AF: 0.657

Asia WGS AF: 0.708 AC: 2460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2841453; hg19: chr9-88014875;