6-33528937-T-G

Variant names:

• chr6-33528937-T-G
• rs449242
• XR_001743876.1:n.17+7034A>C

Variant summary

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

The XR_001743876.1(LOC107986537):​n.17+7034A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,116 control chromosomes in the GnomAD database, including 14,749 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 0.40 (14749 hom., cov: 32)
• Consequence: LOC107986537 XR_001743876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 20 publications found

Genes affected

LOC107986537 (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 = 0.649 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61276 AN: 151998 Hom.: 14707 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.403 AC: 61359 AN: 152116 Hom.: 14749 Cov.: 32 AF XY: 0.390 AC XY: 28972 AN XY: 74380

African (AFR) AF: 0.656 AC: 27207 AN: 41490

American (AMR) AF: 0.339 AC: 5177 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1309 AN: 3470

East Asian (EAS) AF: 0.0793 AC: 411 AN: 5184

South Asian (SAS) AF: 0.189 AC: 910 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2022 AN: 10600

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23116 AN: 67980

Other (OTH) AF: 0.410 AC: 866 AN: 2114

Alfa AF: 0.357 Hom.: 28133

Bravo AF: 0.430

Asia WGS AF: 0.186 AC: 649 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	0.58
DANN	Benign	0.36
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs449242; hg19: chr6-33496714;