20-39846160-T-C

Variant names:

• chr20-39846160-T-C
• rs211841

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.429 in 152,068 control chromosomes in the GnomAD database, including 15,187 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 0.43 (15187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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: 0.429 AC: 65165 AN: 151950 Hom.: 15160 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.429 AC: 65245 AN: 152068 Hom.: 15187 Cov.: 32 AF XY: 0.427 AC XY: 31707 AN XY: 74318

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.360

Alfa AF: 0.349 Hom.: 14152

Bravo AF: 0.436

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211841; hg19: chr20-38474802;