rs10831416

Variant names:

• chr11-95734056-A-G
• rs10831416
• ENST00000648353.1:n.526-10663A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648353.1(ENSG00000285842):​n.526-10663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,008 control chromosomes in the GnomAD database, including 8,056 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 0.30 (8056 hom., cov: 31)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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
ENSG00000285842	ENST00000648353.1	n.526-10663A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45161 AN: 151890 Hom.: 8052 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.297 AC: 45168 AN: 152008 Hom.: 8056 Cov.: 31 AF XY: 0.292 AC XY: 21692 AN XY: 74290

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.344

Alfa AF: 0.345 Hom.: 1276

Bravo AF: 0.285

Asia WGS AF: 0.201 AC: 699 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	4.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10831416; hg19: chr11-95467220;