rs6064361

chr20-56265952-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.503 in 152,006 control chromosomes in the GnomAD database, including 21,634 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 0.50 (21634 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 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: 0.503 AC: 76388 AN: 151888 Hom.: 21639 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.503 AC: 76411 AN: 152006 Hom.: 21634 Cov.: 31 AF XY: 0.500 AC XY: 37163 AN XY: 74272

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.544

Alfa AF: 0.554 Hom.: 3908

Bravo AF: 0.480

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	9.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6064361; hg19: chr20-54841008;