rs6136489

Positions:

• chr20-1943088-T-G

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 0.464 in 152,018 control chromosomes in the GnomAD database, including 18,466 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 0.46 (18466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.463 AC: 70378 AN: 151900 Hom.: 18411 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.464 AC: 70498 AN: 152018 Hom.: 18466 Cov.: 32 AF XY: 0.465 AC XY: 34565 AN XY: 74298

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.470

Alfa AF: 0.373 Hom.: 21793

Bravo AF: 0.486

Asia WGS AF: 0.712 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6136489; hg19: chr20-1923734;