11-24070136-A-G

Variant names:

• chr11-24070136-A-G
• rs10834273
• ENST00000834536.1:n.201-8622T>C

Variant summary

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

The ENST00000834536.1(ENSG00000308482):​n.201-8622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,034 control chromosomes in the GnomAD database, including 2,395 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 0.16 (2395 hom., cov: 31)
• Consequence: ENSG00000308482 ENST00000834536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 2 publications found

Genes affected

ENSG00000308482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834536.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308482	ENST00000834536.1		n.201-8622T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23983 AN: 151916 Hom.: 2395 Cov.: 31

Gnomad AFR AF: 0.0394

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.158 AC: 23987 AN: 152034 Hom.: 2395 Cov.: 31 AF XY: 0.160 AC XY: 11912 AN XY: 74290

African (AFR) AF: 0.0393 AC: 1631 AN: 41526

American (AMR) AF: 0.165 AC: 2512 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1980 AN: 5140

South Asian (SAS) AF: 0.206 AC: 996 AN: 4830

European-Finnish (FIN) AF: 0.209 AC: 2200 AN: 10542

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13367 AN: 67976

Other (OTH) AF: 0.152 AC: 320 AN: 2108

Alfa AF: 0.190 Hom.: 4521

Bravo AF: 0.152

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.36
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10834273; hg19: chr11-24091682;