20-7870392-G-T

Variant names:

• chr20-7870392-G-T
• rs6086260

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 0.118 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.118 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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0924

Gnomad4 OTH AF: 0.149

Alfa AF: 0.108 Hom.: 678

Bravo AF: 0.125

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6086260; hg19: chr20-7851039;