rs10128650

Variant names:

• chr11-33910504-A-C
• rs10128650
• ENST00000834606.1:n.318-2579A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-33910504-A-C
• chr11-33910504-A-G

Variant summary

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

The ENST00000834606.1(ENSG00000308500):​n.318-2579A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,206 control chromosomes in the GnomAD database, including 606 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 0.073 (606 hom., cov: 32)
• Consequence: ENSG00000308500 ENST00000834606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

Genes affected

ENSG00000308500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834606.1. 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
	ENSG00000308500	ENST00000834606.1		n.318-2579A>C		intron	N/A
	ENSG00000308500	ENST00000834607.1		n.363-2579A>C		intron	N/A
	ENSG00000308500	ENST00000834608.1		n.319-2579A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11036 AN: 152088 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0468

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0537

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0727 AC: 11063 AN: 152206 Hom.: 606 Cov.: 32 AF XY: 0.0706 AC XY: 5255 AN XY: 74432

African (AFR) AF: 0.156 AC: 6459 AN: 41516

American (AMR) AF: 0.0468 AC: 715 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0548 AC: 264 AN: 4818

European-Finnish (FIN) AF: 0.0240 AC: 255 AN: 10610

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0439 AC: 2982 AN: 67998

Other (OTH) AF: 0.0636 AC: 134 AN: 2108

Alfa AF: 0.0515 Hom.: 391

Bravo AF: 0.0775

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10128650;

hg19: chr11-33932051;