rs6065925

Positions:

• chr20-46105657-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 0.202 in 152,150 control chromosomes in the GnomAD database, including 3,449 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 0.20 (3449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

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 (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.202 AC: 30687 AN: 152032 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30704 AN: 152150 Hom.: 3449 Cov.: 32 AF XY: 0.204 AC XY: 15153 AN XY: 74384

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.196

Alfa AF: 0.236 Hom.: 9042

Bravo AF: 0.192

Asia WGS AF: 0.243 AC: 848 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	3.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6065925; hg19: chr20-44734296;