rs10491518

Variant names:

• chr9-119669548-T-C
• rs10491518
• ENST00000750211.1:n.498-50682A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000750211.1(ENSG00000297691):​n.498-50682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00968 in 152,328 control chromosomes in the GnomAD database, including 12 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 0.0097 (12 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 1 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00968 (1474/152328) while in subpopulation NFE AF = 0.0172 (1172/68022). AF 95% confidence interval is 0.0164. There are 12 homozygotes in GnomAd4. There are 626 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 gene

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
ENSG00000297691	ENST00000750211.1	n.498-50682A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.00965 AC: 1469 AN: 152210 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.00261

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.00484

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.00669

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

GnomAD4 genome AF: 0.00968 AC: 1474 AN: 152328 Hom.: 12 Cov.: 32 AF XY: 0.00840 AC XY: 626 AN XY: 74504

African (AFR) AF: 0.00260 AC: 108 AN: 41572

American (AMR) AF: 0.00497 AC: 76 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4828

European-Finnish (FIN) AF: 0.00480 AC: 51 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0172 AC: 1172 AN: 68022

Other (OTH) AF: 0.00662 AC: 14 AN: 2116

Alfa AF: 0.0157 Hom.: 2

Bravo AF: 0.00900

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10491518; hg19: chr9-122431826;