rs6076072

Positions:

• chr20-23425882-A-C
• chr20-23425882-A-G

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 0.0804 in 152,194 control chromosomes in the GnomAD database, including 650 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 0.080 (650 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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 (AMR) allele frequency at 95% confidence interval = 0.129 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: 0.0804 AC: 12230 AN: 152076 Hom.: 648 Cov.: 33

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0804 AC: 12233 AN: 152194 Hom.: 650 Cov.: 33 AF XY: 0.0805 AC XY: 5988 AN XY: 74390

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0922 Hom.: 466

Bravo AF: 0.0814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6076072; hg19: chr20-23406519;