rs67068737

chr20-45324870-G-Achr20-45324870-G-C

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 0.176 in 152,190 control chromosomes in the GnomAD database, including 2,281 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 0.18 (2281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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: 0.176 AC: 26781 AN: 152070 Hom.: 2278 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.176 AC: 26805 AN: 152190 Hom.: 2281 Cov.: 33 AF XY: 0.172 AC XY: 12795 AN XY: 74416

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0807 Hom.: 112

Bravo AF: 0.179

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.015
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67068737; hg19: chr20-43953510;