rs6014787

chr20-56661502-A-G

Variant summary

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

The variant allele was found at a frequency of 0.405 in 152,070 control chromosomes in the GnomAD database, including 15,491 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 (15491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61433 AN: 151952 Hom.: 15449 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.405 AC: 61523 AN: 152070 Hom.: 15491 Cov.: 32 AF XY: 0.399 AC XY: 29649 AN XY: 74328

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.381

Alfa AF: 0.353 Hom.: 2964

Bravo AF: 0.415

Asia WGS AF: 0.147 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6014787; hg19: chr20-55236558;