rs10502232

Variant names:

• chr11-119919359-A-G
• rs10502232
• ENST00000662653.2:n.600-101A>G

Variant summary

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

The ENST00000662653.2(ENSG00000288047):​n.600-101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 152,308 control chromosomes in the GnomAD database, including 86 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 0.026 (86 hom., cov: 33)
• Consequence: ENSG00000288047 ENST00000662653.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 3 publications found

Genes affected

ENSG00000288047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0263 (4002/152308) while in subpopulation NFE AF = 0.0387 (2630/68022). AF 95% confidence interval is 0.0374. There are 86 homozygotes in GnomAd4. There are 2007 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 86 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369526	XR_948080.3	n.779+5663A>G		intron_variant	Intron 2 of 9
LOC105369526	XR_948081.3	n.780-101A>G		intron_variant	Intron 2 of 11
LOC105369526	XR_948082.3	n.378-10176A>G		intron_variant	Intron 1 of 8
LOC105369526	XR_948083.3	n.377+13637A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288047	ENST00000662653.2	n.600-101A>G		intron_variant	Intron 2 of 2
ENSG00000288047	ENST00000688572.2	n.780-101A>G		intron_variant	Intron 2 of 2
ENSG00000288047	ENST00000701780.1	n.779+5663A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0263 AC: 4004 AN: 152190 Hom.: 86 Cov.: 33

Gnomad AFR AF: 0.00610

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0263 AC: 4002 AN: 152308 Hom.: 86 Cov.: 33 AF XY: 0.0269 AC XY: 2007 AN XY: 74472

African (AFR) AF: 0.00609 AC: 253 AN: 41576

American (AMR) AF: 0.0106 AC: 162 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4832

European-Finnish (FIN) AF: 0.0787 AC: 834 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2630 AN: 68022

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0341 Hom.: 191

Bravo AF: 0.0206

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.6
DANN	Benign	0.85
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs10502232; hg19: chr11-119790068;