rs10502232

chr11-119919359-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000701780.1(ENSG00000288047):n.779+5663A>G variant causes a intron, non coding transcript 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: ENST00000701780.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 86 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369526	XR_948081.3	n.780-101A>G		intron_variant, non_coding_transcript_variant
LOC105369526	XR_948080.3	n.779+5663A>G		intron_variant, non_coding_transcript_variant
LOC105369526	XR_948082.3	n.378-10176A>G		intron_variant, non_coding_transcript_variant
LOC105369526	XR_948083.3	n.377+13637A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701780.1	n.779+5663A>G		intron_variant, non_coding_transcript_variant
	ENST00000662653.1	n.590-101A>G		intron_variant, non_coding_transcript_variant
	ENST00000688572.1	n.780-101A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00609

Gnomad4 AMR AF: 0.0106

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0330 Hom.: 56

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502232; hg19: chr11-119790068;