9-32861994-T-C

Variant names:

• chr9-32861994-T-C
• rs1359719
• ENST00000448273.1:n.429+18A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448273.1(ENSG00000236796):​n.429+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000236796 ENST00000448273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 2 publications found

Genes affected

ENSG00000236796 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236796	ENST00000448273.1	n.429+18A>G		intron_variant	Intron 4 of 11	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.614 AC: 25459 AN: 41468

American (AMR) AF: 0.781 AC: 11938 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2491 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3958 AN: 5172

South Asian (SAS) AF: 0.755 AC: 3642 AN: 4824

European-Finnish (FIN) AF: 0.819 AC: 8688 AN: 10614

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49964 AN: 67994

Other (OTH) AF: 0.699 AC: 1478 AN: 2114

Alfa AF: 0.724 Hom.: 50224

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1359719; hg19: chr9-32861992;