chr9-88188557-G-A

Position:

• chr9-88188557-G-A

Variant summary

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

The ENST00000429076.1(ENSG00000229288):​n.1268C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 198,248 control chromosomes in the GnomAD database, including 2,193 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 0.14 (1780 hom., cov: 33)
  • Exomes 𝑓: 0.12 (413 hom.)
• Consequence: ENSG00000229288 ENST00000429076.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

ENSG00000229288 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100129340		n.88188557G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229288	ENST00000429076.1	n.1268C>T		non_coding_transcript_exon_variant	3/3	6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21465 AN: 152016 Hom.: 1774 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.124 AC: 5741 AN: 46114 Hom.: 413 Cov.: 0 AF XY: 0.122 AC XY: 3154 AN XY: 25804

Gnomad4 AFR exome AF: 0.232

Gnomad4 AMR exome AF: 0.143

Gnomad4 ASJ exome AF: 0.0788

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.121

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.0950

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.141 AC: 21490 AN: 152134 Hom.: 1780 Cov.: 33 AF XY: 0.142 AC XY: 10536 AN XY: 74376

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0981

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0974 Hom.: 1252

Bravo AF: 0.145

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17053864; hg19: chr9-90803472;