chr20-61041582-A-G

Position:

• chr20-61041582-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 0.561 in 152,058 control chromosomes in the GnomAD database, including 24,248 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 0.56 (24248 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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: 0.560 AC: 85152 AN: 151940 Hom.: 24210 Cov.: 33

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.561 AC: 85243 AN: 152058 Hom.: 24248 Cov.: 33 AF XY: 0.560 AC XY: 41660 AN XY: 74336

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.560

Alfa AF: 0.556 Hom.: 3991

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0010
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6101206; hg19: chr20-59616638;