9-129430707-A-G

Position:

• chr9-129430707-A-G

Variant summary

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

The ENST00000436510.1(ENSG00000230676):​n.1791T>C 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 0.198 in 140,200 control chromosomes in the GnomAD database, including 934 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 0.20 (934 hom., cov: 45)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: ENSG00000230676 ENST00000436510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

ENSG00000230676 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129430707A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230676	ENST00000436510.1	n.1791T>C		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 27679 AN: 140068 Hom.: 931 Cov.: 45

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.198 AC: 27692 AN: 140184 Hom.: 934 Cov.: 45 AF XY: 0.201 AC XY: 13689 AN XY: 68248

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.225

Alfa AF: 0.211 Hom.: 7003

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837366; hg19: chr9-132192986;