20-6786995-G-T

Variant names:

• chr20-6786995-G-T
• rs910141

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 0.202 in 152,138 control chromosomes in the GnomAD database, including 3,297 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 0.20 (3297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.203 AC: 30787 AN: 152020 Hom.: 3295 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.202 AC: 30791 AN: 152138 Hom.: 3297 Cov.: 32 AF XY: 0.204 AC XY: 15153 AN XY: 74372

African (AFR) AF: 0.140 AC: 5831 AN: 41514

American (AMR) AF: 0.208 AC: 3183 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3468

East Asian (EAS) AF: 0.0760 AC: 394 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4812

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15940 AN: 67984

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.221 Hom.: 7446

Bravo AF: 0.195

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs910141; hg19: chr20-6767642;