rs236140

Positions:

• chr20-5911226-A-C
• chr20-5911226-A-T

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 0.384 in 152,058 control chromosomes in the GnomAD database, including 11,968 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 (11968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58289 AN: 151938 Hom.: 11952 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.384 AC: 58353 AN: 152058 Hom.: 11968 Cov.: 32 AF XY: 0.391 AC XY: 29054 AN XY: 74344

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.384

Alfa AF: 0.376 Hom.: 1604

Bravo AF: 0.380

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs236140; hg19: chr20-5891872;