11-6728826-C-T

Variant names:

• chr11-6728826-C-T
• rs12799172
• ENST00000526769.4:n.147-6944G>A

Variant summary

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

The ENST00000526769.4(ENSG00000291143):​n.147-6944G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,866 control chromosomes in the GnomAD database, including 6,300 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 0.27 (6300 hom., cov: 31)
• Consequence: ENSG00000291143 ENST00000526769.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 4 publications found

Genes affected

ENSG00000291143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526769.4. 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
	ENSG00000291143	ENST00000526769.4	TSL:1	n.147-6944G>A		intron	N/A
	ENSG00000294763	ENST00000725824.1		n.218-19351C>T		intron	N/A
	ENSG00000294763	ENST00000725825.1		n.231-13528C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40265 AN: 151750 Hom.: 6302 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.265 AC: 40263 AN: 151866 Hom.: 6300 Cov.: 31 AF XY: 0.266 AC XY: 19706 AN XY: 74192

African (AFR) AF: 0.104 AC: 4325 AN: 41416

American (AMR) AF: 0.246 AC: 3748 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3472

East Asian (EAS) AF: 0.179 AC: 924 AN: 5156

South Asian (SAS) AF: 0.202 AC: 973 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4161 AN: 10506

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24070 AN: 67940

Other (OTH) AF: 0.279 AC: 591 AN: 2116

Alfa AF: 0.307 Hom.: 6296

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	3.3
DANN	Benign	0.50
PhyloP100		0.21

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: rs12799172;

hg19: chr11-6750057;