13-33724158-A-G

Variant names:

• chr13-33724158-A-G
• rs7319180
• ENST00000731018.1:n.194+23763A>G

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+23763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,212 control chromosomes in the GnomAD database, including 996 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 0.077 (996 hom., cov: 33)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

Genes affected

ENSG00000295576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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
ENSG00000295576	ENST00000731018.1	n.194+23763A>G		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1	n.51-37675A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11738 AN: 152094 Hom.: 992 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0774 AC: 11776 AN: 152212 Hom.: 996 Cov.: 33 AF XY: 0.0787 AC XY: 5859 AN XY: 74444

African (AFR) AF: 0.191 AC: 7937 AN: 41510

American (AMR) AF: 0.0731 AC: 1118 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5186

South Asian (SAS) AF: 0.0507 AC: 245 AN: 4828

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 751 AN: 68008

Other (OTH) AF: 0.0630 AC: 133 AN: 2110

Alfa AF: 0.0145 Hom.: 16

Bravo AF: 0.0881

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.16
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7319180; hg19: chr13-34298295;