chr13-33723341-C-A

Variant names:

• chr13-33723341-C-A
• rs9598027
• ENST00000731018.1:n.194+22946C>A

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+22946C>A 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 152,130 control chromosomes in the GnomAD database, including 995 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 (995 hom., cov: 32)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731018.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295576	ENST00000731018.1		n.194+22946C>A		intron	N/A
	ENSG00000288767	ENST00000731141.1		n.51-38492C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11738 AN: 152012 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0774 AC: 11776 AN: 152130 Hom.: 995 Cov.: 32 AF XY: 0.0788 AC XY: 5857 AN XY: 74356

African (AFR) AF: 0.191 AC: 7941 AN: 41476

American (AMR) AF: 0.0731 AC: 1116 AN: 15272

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

East Asian (EAS) AF: 0.251 AC: 1298 AN: 5176

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4816

European-Finnish (FIN) AF: 0.0230 AC: 243 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0111 AC: 752 AN: 68014

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0146 Hom.: 16

Bravo AF: 0.0881

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs9598027; hg19: chr13-34297478;