rs6101206

Variant names:

• chr20-61041582-A-G
• rs6101206

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.636 AC: 26387 AN: 41492

American (AMR) AF: 0.628 AC: 9594 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3194 AN: 5148

South Asian (SAS) AF: 0.632 AC: 3046 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4570 AN: 10576

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34646 AN: 67968

Other (OTH) AF: 0.560 AC: 1180 AN: 2106

Alfa AF: 0.559 Hom.: 4158

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0010
DANN	Benign	0.28
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs6101206; hg19: chr20-59616638;