9-32865571-A-G

Variant names:

• chr9-32865571-A-G
• rs6476383
• ENST00000448273.1:n.77-365T>C

Variant summary

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

The ENST00000448273.1(ENSG00000236796):​n.77-365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,256 control chromosomes in the GnomAD database, including 65,400 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 0.92 (65400 hom., cov: 32)
• Consequence: ENSG00000236796 ENST00000448273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.77-365T>C		intron_variant	Intron 1 of 11	6

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140402 AN: 152138 Hom.: 65358 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.923 AC: 140503 AN: 152256 Hom.: 65400 Cov.: 32 AF XY: 0.922 AC XY: 68653 AN XY: 74466

African (AFR) AF: 0.788 AC: 32722 AN: 41506

American (AMR) AF: 0.956 AC: 14630 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3412 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5182

South Asian (SAS) AF: 0.942 AC: 4544 AN: 4822

European-Finnish (FIN) AF: 0.950 AC: 10085 AN: 10614

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66795 AN: 68042

Other (OTH) AF: 0.933 AC: 1974 AN: 2116

Alfa AF: 0.926 Hom.: 11725

Bravo AF: 0.918

Asia WGS AF: 0.966 AC: 3359 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	6.4
DANN	Benign	0.59
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs6476383; hg19: chr9-32865569;