20-39846160-T-C

Variant names:

• chr20-39846160-T-C
• rs211841

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 0.429 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.625 AC: 25936 AN: 41504

American (AMR) AF: 0.368 AC: 5624 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3472

East Asian (EAS) AF: 0.344 AC: 1770 AN: 5152

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4814

European-Finnish (FIN) AF: 0.416 AC: 4386 AN: 10552

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23801 AN: 67976

Other (OTH) AF: 0.360 AC: 760 AN: 2114

Alfa AF: 0.373 Hom.: 27322

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
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs211841; hg19: chr20-38474802;