rs10831416

Positions:

• chr11-95734056-A-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, non coding transcript 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: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648353.1	n.526-10663A>G		intron_variant, non_coding_transcript_variant

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;