rs6092477

chr20-57416639-G-Achr20-57416639-G-Cchr20-57416639-G-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 0.361 in 152,122 control chromosomes in the GnomAD database, including 10,346 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 0.36 (10346 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.361 AC: 54861 AN: 152004 Hom.: 10332 Cov.: 34

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.361 AC: 54920 AN: 152122 Hom.: 10346 Cov.: 34 AF XY: 0.367 AC XY: 27251 AN XY: 74352

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.380

Alfa AF: 0.333 Hom.: 18480

Bravo AF: 0.372

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6092477; hg19: chr20-55991695;