20-39909900-G-T

Variant names:

• chr20-39909900-G-T
• rs11699371

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 0.212 in 152,040 control chromosomes in the GnomAD database, including 3,957 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 0.21 (3957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32236 AN: 151922 Hom.: 3956 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.212 AC: 32247 AN: 152040 Hom.: 3957 Cov.: 32 AF XY: 0.216 AC XY: 16030 AN XY: 74314

African (AFR) AF: 0.101 AC: 4212 AN: 41514

American (AMR) AF: 0.183 AC: 2788 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1454 AN: 5162

South Asian (SAS) AF: 0.172 AC: 827 AN: 4814

European-Finnish (FIN) AF: 0.366 AC: 3862 AN: 10556

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18071 AN: 67932

Other (OTH) AF: 0.178 AC: 376 AN: 2114

Alfa AF: 0.230 Hom.: 7097

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.11
DANN	Benign	0.75
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11699371; hg19: chr20-38538542;