20-6389406-T-G

Variant names:

• chr20-6389406-T-G
• rs1571218

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 0.714 in 152,068 control chromosomes in the GnomAD database, including 39,923 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 0.71 (39923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.714 AC: 108441 AN: 151950 Hom.: 39870 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.714 AC: 108555 AN: 152068 Hom.: 39923 Cov.: 32 AF XY: 0.714 AC XY: 53080 AN XY: 74332

African (AFR) AF: 0.883 AC: 36640 AN: 41512

American (AMR) AF: 0.726 AC: 11100 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4597 AN: 5176

South Asian (SAS) AF: 0.655 AC: 3155 AN: 4816

European-Finnish (FIN) AF: 0.654 AC: 6900 AN: 10550

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41391 AN: 67948

Other (OTH) AF: 0.741 AC: 1562 AN: 2108

Alfa AF: 0.658 Hom.: 18134

Bravo AF: 0.733

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.46
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs1571218; hg19: chr20-6370053;