rs10491833

Variant names:

• chr9-24720234-T-C
• rs10491833
• ENST00000826532.2:n.489-22552T>C

Variant summary

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

The ENST00000826532.2(ENSG00000269957):​n.489-22552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,508 control chromosomes in the GnomAD database, including 2,906 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 0.18 (2906 hom., cov: 31)
• Consequence: ENSG00000269957 ENST00000826532.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 6 publications found

Genes affected

ENSG00000269957 (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 (NFE) allele frequency at 95% confidence interval = 0.232 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
ENSG00000269957	ENST00000826532.2	n.489-22552T>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26801 AN: 151392 Hom.: 2901 Cov.: 31

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.177 AC: 26820 AN: 151508 Hom.: 2906 Cov.: 31 AF XY: 0.179 AC XY: 13207 AN XY: 73988

African (AFR) AF: 0.0566 AC: 2346 AN: 41458

American (AMR) AF: 0.208 AC: 3164 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3462

East Asian (EAS) AF: 0.124 AC: 639 AN: 5156

South Asian (SAS) AF: 0.140 AC: 675 AN: 4816

European-Finnish (FIN) AF: 0.280 AC: 2916 AN: 10418

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 15901 AN: 67686

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.217 Hom.: 2273

Bravo AF: 0.167

Asia WGS AF: 0.154 AC: 534 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	1.2
DANN	Benign	0.45
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs10491833; hg19: chr9-24720232;