20-9911679-T-C

Variant names:

• chr20-9911679-T-C
• rs6057009

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 0.459 in 151,918 control chromosomes in the GnomAD database, including 17,532 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 0.46 (17532 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.458 AC: 69571 AN: 151800 Hom.: 17493 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.459 AC: 69665 AN: 151918 Hom.: 17532 Cov.: 31 AF XY: 0.454 AC XY: 33687 AN XY: 74280

African (AFR) AF: 0.674 AC: 27885 AN: 41392

American (AMR) AF: 0.359 AC: 5479 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5162

South Asian (SAS) AF: 0.394 AC: 1895 AN: 4814

European-Finnish (FIN) AF: 0.358 AC: 3787 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26291 AN: 67938

Other (OTH) AF: 0.465 AC: 982 AN: 2112

Alfa AF: 0.410 Hom.: 41567

Bravo AF: 0.466

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6057009; hg19: chr20-9892327;