6-134817852-C-A

Variant names:

• chr6-134817852-C-A
• rs2049953
• ENST00000836833.1:n.212-12059G>T

Variant summary

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

The ENST00000836833.1(ENSG00000308852):​n.212-12059G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,204 control chromosomes in the GnomAD database, including 45,884 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 0.77 (45884 hom., cov: 33)
• Consequence: ENSG00000308852 ENST00000836833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 11 publications found

Genes affected

ENSG00000308852 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836833.1. 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
	ENSG00000308852	ENST00000836833.1		n.212-12059G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117718 AN: 152086 Hom.: 45849 Cov.: 33

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.774 AC: 117806 AN: 152204 Hom.: 45884 Cov.: 33 AF XY: 0.780 AC XY: 58036 AN XY: 74410

African (AFR) AF: 0.846 AC: 35136 AN: 41532

American (AMR) AF: 0.801 AC: 12245 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4257 AN: 5188

South Asian (SAS) AF: 0.721 AC: 3475 AN: 4822

European-Finnish (FIN) AF: 0.841 AC: 8915 AN: 10602

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48951 AN: 67984

Other (OTH) AF: 0.755 AC: 1595 AN: 2112

Alfa AF: 0.736 Hom.: 195473

Bravo AF: 0.776

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.69
DANN	Benign	0.50
PhyloP100		-0.15

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: rs2049953;

hg19: chr6-135138990;