20-39952870-T-G

Variant names:

• chr20-39952870-T-G
• rs11699530

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.342 in 151,962 control chromosomes in the GnomAD database, including 9,042 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 0.34 (9042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.342 AC: 51995 AN: 151844 Hom.: 9039 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.342 AC: 52025 AN: 151962 Hom.: 9042 Cov.: 31 AF XY: 0.343 AC XY: 25489 AN XY: 74288

African (AFR) AF: 0.365 AC: 15111 AN: 41428

American (AMR) AF: 0.306 AC: 4675 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1617 AN: 5150

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4137 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23399 AN: 67952

Other (OTH) AF: 0.316 AC: 663 AN: 2100

Alfa AF: 0.334 Hom.: 20703

Bravo AF: 0.339

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	9.3
DANN	Benign	0.58
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11699530; hg19: chr20-38581512;