9-86760399-C-T

Variant names:

• chr9-86760399-C-T
• rs994029
• ENST00000824591.1:n.406-7057C>T

Variant summary

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

The ENST00000824591.1(ENSG00000288575):​n.406-7057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,178 control chromosomes in the GnomAD database, including 38,630 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 0.70 (38630 hom., cov: 34)
• Consequence: ENSG00000288575 ENST00000824591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 3 publications found

Genes affected

ENSG00000288575 (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 = 0.859 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
ENSG00000288575	ENST00000824591.1	n.406-7057C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106832 AN: 152060 Hom.: 38580 Cov.: 34

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.703 AC: 106938 AN: 152178 Hom.: 38630 Cov.: 34 AF XY: 0.706 AC XY: 52485 AN XY: 74382

African (AFR) AF: 0.866 AC: 35982 AN: 41534

American (AMR) AF: 0.668 AC: 10214 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4441 AN: 5190

South Asian (SAS) AF: 0.605 AC: 2912 AN: 4816

European-Finnish (FIN) AF: 0.692 AC: 7316 AN: 10570

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42130 AN: 67986

Other (OTH) AF: 0.640 AC: 1354 AN: 2114

Alfa AF: 0.637 Hom.: 51264

Bravo AF: 0.712

Asia WGS AF: 0.746 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs994029; hg19: chr9-89375314; COSMIC: COSV68657273;