rs6065912

Positions:

• chr20-46003728-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 0.122 in 152,182 control chromosomes in the GnomAD database, including 1,175 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 0.12 (1175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 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: 0.122 AC: 18531 AN: 152064 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.122 AC: 18542 AN: 152182 Hom.: 1175 Cov.: 32 AF XY: 0.122 AC XY: 9059 AN XY: 74414

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0747

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.125

Alfa AF: 0.124 Hom.: 1169

Bravo AF: 0.116

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
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: rs6065912; hg19: chr20-44632367;