9-69089911-C-T

Variant names:

• chr9-69089911-C-T
• rs953588
• ENST00000642889.1:c.166-9990C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642889.1(ENSG00000285130):​c.166-9990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,948 control chromosomes in the GnomAD database, including 9,002 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 0.34 (9002 hom., cov: 32)
• Consequence: ENSG00000285130 ENST00000642889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

ENSG00000285130 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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
ENSG00000285130	ENST00000642889.1	c.166-9990C>T		intron_variant	Intron 1 of 24			ENSP00000493780.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51839 AN: 151828 Hom.: 8999 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.341 AC: 51857 AN: 151948 Hom.: 9002 Cov.: 32 AF XY: 0.342 AC XY: 25371 AN XY: 74280

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.368

Alfa AF: 0.344 Hom.: 5219

Bravo AF: 0.333

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953588; hg19: chr9-71704827;