rs2049953

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-134817852-C-A
• chr6-134817852-C-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928277	XR_001744363.2	n.340-12059G>T		intron_variant	Intron 1 of 3
LOC101928277	XR_001744364.2	n.287-12059G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308852	ENST00000836833.1	n.212-12059G>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2049953; hg19: chr6-135138990;