rs6107905

chr20-6998506-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 0.648 in 152,110 control chromosomes in the GnomAD database, including 36,817 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 0.65 (36817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

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 = 0.841 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: 0.649 AC: 98611 AN: 151994 Hom.: 36815 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.648 AC: 98626 AN: 152110 Hom.: 36817 Cov.: 32 AF XY: 0.655 AC XY: 48706 AN XY: 74360

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.687

Alfa AF: 0.756 Hom.: 12043

Bravo AF: 0.625

Asia WGS AF: 0.749 AC: 2604 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	3.5
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6107905; hg19: chr20-6979153;