rs4529888

Variant names:

• chr11-127211696-G-A
• rs4529888
• ENST00000609845.1:n.306-11536G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-127211696-G-A
• chr11-127211696-G-C

Variant summary

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

The ENST00000609845.1(ENSG00000272642):​n.306-11536G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,068 control chromosomes in the GnomAD database, including 36,042 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 0.68 (36042 hom., cov: 32)
• Consequence: ENSG00000272642 ENST00000609845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 4 publications found

Genes affected

ENSG00000272642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609845.1. 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
	ENSG00000272642	ENST00000609845.1	TSL:3	n.306-11536G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103196 AN: 151950 Hom.: 35989 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.679 AC: 103311 AN: 152068 Hom.: 36042 Cov.: 32 AF XY: 0.685 AC XY: 50927 AN XY: 74316

African (AFR) AF: 0.798 AC: 33125 AN: 41500

American (AMR) AF: 0.707 AC: 10822 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1977 AN: 3464

East Asian (EAS) AF: 0.942 AC: 4869 AN: 5170

South Asian (SAS) AF: 0.716 AC: 3452 AN: 4818

European-Finnish (FIN) AF: 0.675 AC: 7106 AN: 10532

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.586 AC: 39801 AN: 67968

Other (OTH) AF: 0.627 AC: 1326 AN: 2114

Alfa AF: 0.622 Hom.: 89512

Bravo AF: 0.689

Asia WGS AF: 0.857 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.49

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: rs4529888;

hg19: chr11-127081591;