13-46826872-T-C

Variant names:

• chr13-46826872-T-C
• rs9567732
• ENST00000783844.1:n.96-4424T>C

Variant summary

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

The ENST00000783844.1(ENSG00000302073):​n.96-4424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,032 control chromosomes in the GnomAD database, including 38,609 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 0.70 (38609 hom., cov: 32)
• Consequence: ENSG00000302073 ENST00000783844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 6 publications found

Genes affected

ENSG00000302073 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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
ENSG00000302073	ENST00000783844.1	n.96-4424T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105944 AN: 151914 Hom.: 38581 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.697 AC: 106025 AN: 152032 Hom.: 38609 Cov.: 32 AF XY: 0.692 AC XY: 51398 AN XY: 74298

African (AFR) AF: 0.905 AC: 37597 AN: 41528

American (AMR) AF: 0.692 AC: 10584 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2568 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3843 AN: 5170

South Asian (SAS) AF: 0.581 AC: 2795 AN: 4814

European-Finnish (FIN) AF: 0.492 AC: 5191 AN: 10542

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41200 AN: 67904

Other (OTH) AF: 0.703 AC: 1486 AN: 2114

Alfa AF: 0.646 Hom.: 87357

Bravo AF: 0.726

Asia WGS AF: 0.659 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9567732; hg19: chr13-47401007;