9-32861994-T-C

Position:

• chr9-32861994-T-C

Variant summary

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

The variant allele was found at a frequency of 0.712 in 152,156 control chromosomes in the GnomAD database, including 39,003 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 0.71 (39002 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32861994T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236796	ENST00000448273.1	n.429+18A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108279 AN: 152028 Hom.: 38970 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.712 AC: 108368 AN: 152148 Hom.: 39002 Cov.: 33 AF XY: 0.717 AC XY: 53352 AN XY: 74396

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.699

Alfa AF: 0.728 Hom.: 38656

Bravo AF: 0.704

Asia WGS AF: 0.748 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359719; hg19: chr9-32861992;