chr3-32800609-T-G

Variant names:

• chr3-32800609-T-G
• rs9845475
• ENST00000791322.1:n.360-11409A>C

Variant summary

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

The ENST00000791322.1(ENSG00000303033):​n.360-11409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,006 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 31)
• Consequence: ENSG00000303033 ENST00000791322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 11 publications found

Genes affected

ENSG00000303033 (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 (NFE) allele frequency at 95% confidence interval = 0.138 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
ENSG00000303033	ENST00000791322.1	n.360-11409A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16684 AN: 151888 Hom.: 1052 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.110 AC: 16703 AN: 152006 Hom.: 1052 Cov.: 31 AF XY: 0.110 AC XY: 8157 AN XY: 74304

African (AFR) AF: 0.0684 AC: 2839 AN: 41480

American (AMR) AF: 0.0913 AC: 1390 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5166

South Asian (SAS) AF: 0.138 AC: 665 AN: 4814

European-Finnish (FIN) AF: 0.0889 AC: 939 AN: 10566

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.140 AC: 9538 AN: 67970

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.127 Hom.: 2764

Bravo AF: 0.107

Asia WGS AF: 0.0620 AC: 217 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	3.1
DANN	Benign	0.77
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9845475; hg19: chr3-32842101;