rs156331

Variant names:

• chr20-1846342-C-A
• rs156331

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;