rs17329669

Variant names:

• chr7-36812324-A-G
• rs17329669
• ENST00000829529.1:n.742+15662A>G

Variant summary

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

The ENST00000829529.1(ENSG00000230831):​n.742+15662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,958 control chromosomes in the GnomAD database, including 1,198 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 0.11 (1198 hom., cov: 31)
• Consequence: ENSG00000230831 ENST00000829529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 4 publications found

Genes affected

ENSG00000230831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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
ENSG00000230831	ENST00000829529.1	n.742+15662A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17424 AN: 151840 Hom.: 1197 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.115 AC: 17452 AN: 151958 Hom.: 1198 Cov.: 31 AF XY: 0.111 AC XY: 8265 AN XY: 74242

African (AFR) AF: 0.0748 AC: 3101 AN: 41442

American (AMR) AF: 0.101 AC: 1542 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3472

East Asian (EAS) AF: 0.00446 AC: 23 AN: 5162

South Asian (SAS) AF: 0.201 AC: 962 AN: 4798

European-Finnish (FIN) AF: 0.0738 AC: 779 AN: 10562

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9870 AN: 67948

Other (OTH) AF: 0.135 AC: 285 AN: 2110

Alfa AF: 0.138 Hom.: 1938

Bravo AF: 0.112

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs17329669; hg19: chr7-36851929;