chr20-39979613-T-G

Variant names:

• chr20-39979613-T-G
• rs6124201

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.486 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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.507

Alfa AF: 0.512 Hom.: 19929

Bravo AF: 0.477

Asia WGS AF: 0.605 AC: 2069 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6124201; hg19: chr20-38608255;