rs6137473

Variant names:

• chr20-21904055-G-A
• rs6137473

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 0.605 in 151,956 control chromosomes in the GnomAD database, including 28,418 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 0.60 (28418 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.605 AC: 91818 AN: 151838 Hom.: 28391 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.605 AC: 91892 AN: 151956 Hom.: 28418 Cov.: 31 AF XY: 0.604 AC XY: 44877 AN XY: 74254

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.559

Alfa AF: 0.562 Hom.: 33476

Bravo AF: 0.601

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.028
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6137473; hg19: chr20-21884693;