20-6718948-T-G

Variant names:

• chr20-6718948-T-G
• rs4813802

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 0.283 in 152,016 control chromosomes in the GnomAD database, including 7,024 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 0.28 (7024 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 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: 0.283 AC: 42987 AN: 151898 Hom.: 7016 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 42996 AN: 152016 Hom.: 7024 Cov.: 31 AF XY: 0.286 AC XY: 21225 AN XY: 74304

African (AFR) AF: 0.123 AC: 5089 AN: 41460

American (AMR) AF: 0.351 AC: 5357 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5162

South Asian (SAS) AF: 0.446 AC: 2145 AN: 4806

European-Finnish (FIN) AF: 0.325 AC: 3428 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23776 AN: 67972

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.320 Hom.: 19537

Bravo AF: 0.277

Asia WGS AF: 0.311 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Benign	0.66
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs4813802; hg19: chr20-6699595;