13-33723542-A-C

Variant names:

• chr13-33723542-A-C
• rs9598029
• ENST00000731018.1:n.194+23147A>C

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+23147A>C 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 152,066 control chromosomes in the GnomAD database, including 993 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 (993 hom., cov: 32)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 3 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=-0.91).
• 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+23147A>C		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1	n.51-38291A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11729 AN: 151948 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0774 AC: 11767 AN: 152066 Hom.: 993 Cov.: 32 AF XY: 0.0786 AC XY: 5844 AN XY: 74358

African (AFR) AF: 0.192 AC: 7940 AN: 41436

American (AMR) AF: 0.0733 AC: 1119 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5162

South Asian (SAS) AF: 0.0506 AC: 244 AN: 4820

European-Finnish (FIN) AF: 0.0231 AC: 244 AN: 10576

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

European-Non Finnish (NFE) AF: 0.0110 AC: 749 AN: 68006

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0342 Hom.: 1566

Bravo AF: 0.0881

Asia WGS AF: 0.175 AC: 606 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	0.21
DANN	Benign	0.52
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9598029; hg19: chr13-34297679;