rs6065259

Variant names:

• chr20-40633339-G-A
• rs6065259
• XR_001754596.2:n.243+2249C>T

Variant summary

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

The XR_001754596.2(LOC102724968):​n.243+2249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,108 control chromosomes in the GnomAD database, including 11,046 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 0.38 (11046 hom., cov: 33)
• Consequence: LOC102724968 XR_001754596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 10 publications found

Genes affected

LOC102724968 (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 = 0.406 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: 0.378 AC: 57468 AN: 151990 Hom.: 11055 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.378 AC: 57467 AN: 152108 Hom.: 11046 Cov.: 33 AF XY: 0.381 AC XY: 28312 AN XY: 74350

African (AFR) AF: 0.292 AC: 12103 AN: 41500

American (AMR) AF: 0.397 AC: 6063 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2150 AN: 5148

South Asian (SAS) AF: 0.378 AC: 1826 AN: 4826

European-Finnish (FIN) AF: 0.436 AC: 4612 AN: 10576

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27865 AN: 67982

Other (OTH) AF: 0.365 AC: 771 AN: 2114

Alfa AF: 0.398 Hom.: 6350

Bravo AF: 0.372

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6065259; hg19: chr20-39261979;