chr20-34141638-T-G

Variant names:

• chr20-34141638-T-G
• rs4911414

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 0.734 in 151,948 control chromosomes in the GnomAD database, including 41,496 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 0.73 (41496 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 87 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111420 AN: 151830 Hom.: 41444 Cov.: 30

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.734 AC: 111525 AN: 151948 Hom.: 41496 Cov.: 30 AF XY: 0.742 AC XY: 55158 AN XY: 74290

African (AFR) AF: 0.848 AC: 35137 AN: 41448

American (AMR) AF: 0.705 AC: 10765 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2651 AN: 3466

East Asian (EAS) AF: 0.824 AC: 4268 AN: 5182

South Asian (SAS) AF: 0.850 AC: 4096 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7754 AN: 10502

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44508 AN: 67944

Other (OTH) AF: 0.745 AC: 1571 AN: 2110

Alfa AF: 0.688 Hom.: 116407

Bravo AF: 0.735

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.43
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4911414; hg19: chr20-32729444;