chr20-7033798-T-C

Variant names:

• chr20-7033798-T-C
• rs2149642

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 0.282 in 152,078 control chromosomes in the GnomAD database, including 6,587 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 (6587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.281 AC: 42768 AN: 151960 Hom.: 6571 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.282 AC: 42831 AN: 152078 Hom.: 6587 Cov.: 31 AF XY: 0.282 AC XY: 20940 AN XY: 74346

African (AFR) AF: 0.411 AC: 17049 AN: 41460

American (AMR) AF: 0.265 AC: 4043 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1728 AN: 5160

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10604

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15079 AN: 67978

Other (OTH) AF: 0.287 AC: 604 AN: 2104

Alfa AF: 0.247 Hom.: 20746

Bravo AF: 0.294

Asia WGS AF: 0.342 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.30
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2149642; hg19: chr20-7014445;