rs6132819

Variant names:

• chr20-25237982-G-C
• rs6132819
• XR_001754564.3:n.6485C>G

Variant summary

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

The XR_001754564.3(LOC105372579):​n.6485C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,062 control chromosomes in the GnomAD database, including 12,955 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 0.39 (12955 hom., cov: 32)
• Consequence: LOC105372579 XR_001754564.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 11 publications found

Genes affected

LOC105372579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59118 AN: 151944 Hom.: 12956 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.389 AC: 59126 AN: 152062 Hom.: 12955 Cov.: 32 AF XY: 0.393 AC XY: 29171 AN XY: 74300

African (AFR) AF: 0.237 AC: 9825 AN: 41492

American (AMR) AF: 0.343 AC: 5246 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3468

East Asian (EAS) AF: 0.919 AC: 4755 AN: 5176

South Asian (SAS) AF: 0.443 AC: 2130 AN: 4812

European-Finnish (FIN) AF: 0.453 AC: 4778 AN: 10556

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29908 AN: 67960

Other (OTH) AF: 0.382 AC: 806 AN: 2112

Alfa AF: 0.410 Hom.: 1676

Bravo AF: 0.376

Asia WGS AF: 0.651 AC: 2261 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.66
DANN	Benign	0.46
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6132819; hg19: chr20-25218618;