chr13-109373289-T-G

Variant names:

• chr13-109373289-T-G
• rs9521337
• ENST00000750929.1:n.112-15075A>C

Variant summary

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

The ENST00000750929.1(ENSG00000297783):​n.112-15075A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,054 control chromosomes in the GnomAD database, including 46,905 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 0.77 (46905 hom., cov: 31)
• Consequence: ENSG00000297783 ENST00000750929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 1 publications found

Genes affected

ENSG00000297783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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
ENSG00000297783	ENST00000750929.1	n.112-15075A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116677 AN: 151936 Hom.: 46881 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.768 AC: 116748 AN: 152054 Hom.: 46905 Cov.: 31 AF XY: 0.772 AC XY: 57361 AN XY: 74328

African (AFR) AF: 0.501 AC: 20768 AN: 41434

American (AMR) AF: 0.849 AC: 12958 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2797 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5157 AN: 5162

South Asian (SAS) AF: 0.828 AC: 3992 AN: 4820

European-Finnish (FIN) AF: 0.881 AC: 9323 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58990 AN: 68010

Other (OTH) AF: 0.787 AC: 1660 AN: 2108

Alfa AF: 0.761 Hom.: 2595

Bravo AF: 0.757

Asia WGS AF: 0.911 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9521337; hg19: chr13-110025636;