20-7012982-T-C

Variant names:

• chr20-7012982-T-C
• rs6038683

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 0.909 in 152,082 control chromosomes in the GnomAD database, including 63,728 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 0.91 (63728 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138117 AN: 151964 Hom.: 63688 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.909 AC: 138216 AN: 152082 Hom.: 63728 Cov.: 31 AF XY: 0.911 AC XY: 67713 AN XY: 74358

African (AFR) AF: 0.731 AC: 30282 AN: 41446

American (AMR) AF: 0.958 AC: 14619 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3428 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5055 AN: 5172

South Asian (SAS) AF: 0.982 AC: 4739 AN: 4826

European-Finnish (FIN) AF: 0.970 AC: 10271 AN: 10588

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66678 AN: 67998

Other (OTH) AF: 0.928 AC: 1959 AN: 2112

Alfa AF: 0.970 Hom.: 26166

Bravo AF: 0.901

Asia WGS AF: 0.963 AC: 3326 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs6038683; hg19: chr20-6993629;