20-39979613-T-G

Variant names:

• chr20-39979613-T-G
• rs6124201

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 0.485 in 143,470 control chromosomes in the GnomAD database, including 17,260 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 0.49 (17260 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 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: 0.486 AC: 69641 AN: 143440 Hom.: 17250 Cov.: 23

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.485 AC: 69650 AN: 143470 Hom.: 17260 Cov.: 23 AF XY: 0.486 AC XY: 33684 AN XY: 69250

African (AFR) AF: 0.391 AC: 15175 AN: 38808

American (AMR) AF: 0.482 AC: 6968 AN: 14464

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2038 AN: 3436

East Asian (EAS) AF: 0.514 AC: 2524 AN: 4910

South Asian (SAS) AF: 0.659 AC: 3008 AN: 4564

European-Finnish (FIN) AF: 0.464 AC: 3553 AN: 7660

Middle Eastern (MID) AF: 0.693 AC: 190 AN: 274

European-Non Finnish (NFE) AF: 0.522 AC: 34697 AN: 66460

Other (OTH) AF: 0.507 AC: 1016 AN: 2002

Alfa AF: 0.511 Hom.: 24640

Bravo AF: 0.477

Asia WGS AF: 0.605 AC: 2069 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.23
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs6124201; hg19: chr20-38608255;