chr9-32532471-A-C

Position:

• chr9-32532471-A-C

Variant summary

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

The ENST00000681750.1(ENSG00000288684):​c.-45+18303T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,978 control chromosomes in the GnomAD database, including 20,358 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 0.51 (20358 hom., cov: 32)
• Consequence: ENSG00000288684 ENST00000681750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

ENSG00000288684 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32532471A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288684	ENST00000681750.1	c.-45+18303T>G		intron_variant				ENSP00000506413.1
ENSG00000288684	ENST00000680198.1	c.198+18303T>G		intron_variant				ENSP00000505143.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77624 AN: 151860 Hom.: 20334 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.484

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77685 AN: 151978 Hom.: 20358 Cov.: 32 AF XY: 0.507 AC XY: 37634 AN XY: 74290

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.479

Alfa AF: 0.484 Hom.: 30654

Bravo AF: 0.515

Asia WGS AF: 0.450 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs626214; hg19: chr9-32532469;