rs13290799

Variant names:

• chr9-29545877-C-T
• rs13290799
• ENST00000850880.1:n.99-6890C>T

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.99-6890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,070 control chromosomes in the GnomAD database, including 1,669 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 0.14 (1669 hom., cov: 31)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 5 publications found

Genes affected

ENSG00000300941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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
ENSG00000300941	ENST00000850880.1	n.99-6890C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21282 AN: 151952 Hom.: 1668 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.140 AC: 21304 AN: 152070 Hom.: 1669 Cov.: 31 AF XY: 0.139 AC XY: 10331 AN XY: 74296

African (AFR) AF: 0.0838 AC: 3478 AN: 41492

American (AMR) AF: 0.144 AC: 2201 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3460

East Asian (EAS) AF: 0.0722 AC: 373 AN: 5164

South Asian (SAS) AF: 0.0974 AC: 469 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10566

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11546 AN: 67986

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.159 Hom.: 8591

Bravo AF: 0.135

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.82
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs13290799; hg19: chr9-29545875;