9-98863594-A-T

Variant names:

• chr9-98863594-A-T
• rs7470086
• ENST00000433997.1:n.90+8595T>A

Variant summary

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

The ENST00000433997.1(ENSG00000267026):​n.90+8595T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 151,926 control chromosomes in the GnomAD database, including 43,206 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 0.75 (43206 hom., cov: 30)
• Consequence: ENSG00000267026 ENST00000433997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 3 publications found

Genes affected

ENSG00000267026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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
ENSG00000267026	ENST00000433997.1	n.90+8595T>A		intron_variant	Intron 1 of 1	2
ENSG00000267026	ENST00000590015.5	n.416-1082T>A		intron_variant	Intron 4 of 4	5
ENSG00000267026	ENST00000628879.2	n.315+3091T>A		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114073 AN: 151808 Hom.: 43158 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.752 AC: 114178 AN: 151926 Hom.: 43206 Cov.: 30 AF XY: 0.753 AC XY: 55925 AN XY: 74230

African (AFR) AF: 0.762 AC: 31534 AN: 41384

American (AMR) AF: 0.778 AC: 11874 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5173 AN: 5188

South Asian (SAS) AF: 0.733 AC: 3523 AN: 4804

European-Finnish (FIN) AF: 0.754 AC: 7947 AN: 10538

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49777 AN: 67978

Other (OTH) AF: 0.707 AC: 1490 AN: 2108

Alfa AF: 0.755 Hom.: 5440

Bravo AF: 0.755

Asia WGS AF: 0.889 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.83
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7470086; hg19: chr9-101625876;