rs6064361

Variant names:

• chr20-56265952-T-C
• rs6064361

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;