11-95732995-A-G

Variant names:

• chr11-95732995-A-G
• rs10831415
• ENST00000648353.1:n.526-11724A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648353.1(ENSG00000285842):​n.526-11724A>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 150,984 control chromosomes in the GnomAD database, including 8,029 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 (8029 hom., cov: 28)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 6 publications found

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648353.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285842	ENST00000648353.1		n.526-11724A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 44889 AN: 150866 Hom.: 8025 Cov.: 28

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.297 AC: 44896 AN: 150984 Hom.: 8029 Cov.: 28 AF XY: 0.292 AC XY: 21514 AN XY: 73666

African (AFR) AF: 0.110 AC: 4519 AN: 41152

American (AMR) AF: 0.288 AC: 4354 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1134 AN: 5086

South Asian (SAS) AF: 0.141 AC: 673 AN: 4772

European-Finnish (FIN) AF: 0.383 AC: 3973 AN: 10376

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27501 AN: 67704

Other (OTH) AF: 0.345 AC: 720 AN: 2088

Alfa AF: 0.372 Hom.: 42178

Bravo AF: 0.285

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10831415; hg19: chr11-95466159;