chr20-62476223-G-A

Position:

• chr20-62476223-G-A

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 0.054 in 152,248 control chromosomes in the GnomAD database, including 528 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 0.054 (528 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62476223G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8196 AN: 152130 Hom.: 524 Cov.: 34

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00863

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0540 AC: 8215 AN: 152248 Hom.: 528 Cov.: 34 AF XY: 0.0549 AC XY: 4091 AN XY: 74454

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.00951

Gnomad4 EAS AF: 0.0449

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00863

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0346 Hom.: 45

Bravo AF: 0.0563

Asia WGS AF: 0.111 AC: 385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77067995; hg19: chr20-61051279;