20-51168085-T-C

Variant names:

• chr20-51168085-T-C
• rs16995794

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 0.376 in 151,872 control chromosomes in the GnomAD database, including 10,928 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 0.38 (10928 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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: 0.376 AC: 56984 AN: 151754 Hom.: 10915 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.376 AC: 57035 AN: 151872 Hom.: 10928 Cov.: 31 AF XY: 0.374 AC XY: 27747 AN XY: 74204

African (AFR) AF: 0.440 AC: 18214 AN: 41390

American (AMR) AF: 0.325 AC: 4959 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1047 AN: 5156

South Asian (SAS) AF: 0.275 AC: 1316 AN: 4786

European-Finnish (FIN) AF: 0.408 AC: 4297 AN: 10540

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24760 AN: 67934

Other (OTH) AF: 0.366 AC: 772 AN: 2112

Alfa AF: 0.369 Hom.: 5191

Bravo AF: 0.374

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs16995794; hg19: chr20-49784622;