rs156331

chr20-1846342-C-A

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 0.255 in 152,184 control chromosomes in the GnomAD database, including 5,411 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 0.25 (5411 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38748 AN: 152066 Hom.: 5403 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.255 AC: 38789 AN: 152184 Hom.: 5411 Cov.: 33 AF XY: 0.255 AC XY: 19006 AN XY: 74400

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.269

Alfa AF: 0.205 Hom.: 4720

Bravo AF: 0.259

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs156331; hg19: chr20-1826988;