chr9-113616479-G-A

Position:

• chr9-113616479-G-A

Variant summary

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

The ENST00000635661.1(ENSG00000282897):​n.897C>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 0.798 in 152,318 control chromosomes in the GnomAD database, including 48,741 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 0.80 (48717 hom., cov: 33)
  • Exomes 𝑓: 0.72 (24 hom.)
• Consequence: ENSG00000282897 ENST00000635661.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

ENSG00000282897 (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 (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376222	XR_007061739.1	n.504-756G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282897	ENST00000635661.1	n.897C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121412 AN: 152112 Hom.: 48673 Cov.: 33

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.795

GnomAD4 exome AF: 0.716 AC: 63 AN: 88 Hom.: 24 Cov.: 0 AF XY: 0.742 AC XY: 49 AN XY: 66

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.705

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.798 AC: 121508 AN: 152230 Hom.: 48717 Cov.: 33 AF XY: 0.804 AC XY: 59834 AN XY: 74424

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.797

Alfa AF: 0.791 Hom.: 20750

Bravo AF: 0.800

Asia WGS AF: 0.950 AC: 3300 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	0.24
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs664850; hg19: chr9-116378759;