chr20-56244723-A-T

Variant names:

• chr20-56244723-A-T
• rs6014646

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 0.423 in 151,978 control chromosomes in the GnomAD database, including 14,886 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 (14886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64243 AN: 151860 Hom.: 14844 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.423 AC: 64342 AN: 151978 Hom.: 14886 Cov.: 32 AF XY: 0.423 AC XY: 31422 AN XY: 74290

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.368

Alfa AF: 0.374 Hom.: 1377

Bravo AF: 0.424

Asia WGS AF: 0.408 AC: 1419 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	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6014646; hg19: chr20-54819779;