chr9-85395765-T-A

Variant names:

• chr9-85395765-T-A
• rs2593017
• ENST00000648131.1:n.600+5920A>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+5920A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,242 control chromosomes in the GnomAD database, including 58,650 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 0.88 (58650 hom., cov: 32)
• Consequence: ENSG00000285634 ENST00000648131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285634	ENST00000648131.1	n.600+5920A>T		intron_variant	Intron 3 of 3
ENSG00000285634	ENST00000662737.1	n.1680+5690A>T		intron_variant	Intron 2 of 2
ENSG00000285634	ENST00000669133.1	n.282+6782A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133173 AN: 152124 Hom.: 58607 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.875 AC: 133273 AN: 152242 Hom.: 58650 Cov.: 32 AF XY: 0.876 AC XY: 65170 AN XY: 74422

African (AFR) AF: 0.949 AC: 39429 AN: 41562

American (AMR) AF: 0.756 AC: 11546 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3008 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4851 AN: 5174

South Asian (SAS) AF: 0.904 AC: 4356 AN: 4820

European-Finnish (FIN) AF: 0.890 AC: 9436 AN: 10604

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57828 AN: 68018

Other (OTH) AF: 0.878 AC: 1857 AN: 2114

Alfa AF: 0.869 Hom.: 6720

Bravo AF: 0.867

Asia WGS AF: 0.927 AC: 3223 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	0.079
DANN	Benign	0.56
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2593017; hg19: chr9-88010680;