rs6068566

Positions:

• 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, non coding transcript 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: ENST00000558738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558738.1	n.206+1007C>T		intron_variant, non_coding_transcript_variant		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;