rs6094710

chr20-47466905-G-A

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 0.049 in 152,180 control chromosomes in the GnomAD database, including 224 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 0.049 (224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 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: 0.0491 AC: 7461 AN: 152062 Hom.: 225 Cov.: 31

Gnomad AFR AF: 0.0688

Gnomad AMI AF: 0.0848

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0490 AC: 7459 AN: 152180 Hom.: 224 Cov.: 31 AF XY: 0.0474 AC XY: 3527 AN XY: 74408

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0528 Hom.: 132

Bravo AF: 0.0516

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.86
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6094710; hg19: chr20-46095649;