rs6068566

Variant names:

• chr20-53503102-G-A
• rs6068566
• ENST00000558738.1:n.206+1007C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-53503102-G-A
• chr20-53503102-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558738.1(ENSG00000259723):​n.206+1007C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,796 control chromosomes in the GnomAD database, including 13,484 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 0.42 (13484 hom., cov: 32)
• Consequence: ENSG00000259723 ENST00000558738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

ENSG00000259723 (HGNC:58099):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259723	ENST00000558738.1	n.206+1007C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63551 AN: 151678 Hom.: 13463 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.419 AC: 63620 AN: 151796 Hom.: 13484 Cov.: 32 AF XY: 0.424 AC XY: 31478 AN XY: 74182

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.409

Alfa AF: 0.412 Hom.: 3300

Bravo AF: 0.417

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6068566; hg19: chr20-52119641;