20-7870392-G-T

Variant names:

• chr20-7870392-G-T
• rs6086260

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 0.118 in 152,096 control chromosomes in the GnomAD database, including 1,254 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 0.12 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.309 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: 0.118 AC: 17983 AN: 151978 Hom.: 1247 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.118 AC: 18008 AN: 152096 Hom.: 1254 Cov.: 32 AF XY: 0.120 AC XY: 8907 AN XY: 74352

African (AFR) AF: 0.132 AC: 5462 AN: 41508

American (AMR) AF: 0.158 AC: 2405 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3470

East Asian (EAS) AF: 0.158 AC: 814 AN: 5158

South Asian (SAS) AF: 0.323 AC: 1551 AN: 4806

European-Finnish (FIN) AF: 0.0496 AC: 525 AN: 10590

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6281 AN: 67992

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.105 Hom.: 873

Bravo AF: 0.125

Asia WGS AF: 0.262 AC: 909 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	3.9
DANN	Benign	0.73
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6086260; hg19: chr20-7851039;