rs1320561

Positions:

• chr20-23117243-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 0.514 in 152,072 control chromosomes in the GnomAD database, including 21,078 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 0.51 (21078 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994

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 = 0.585 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: 0.514 AC: 78139 AN: 151954 Hom.: 21063 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.514 AC: 78170 AN: 152072 Hom.: 21078 Cov.: 33 AF XY: 0.506 AC XY: 37632 AN XY: 74328

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.565

Alfa AF: 0.580 Hom.: 43252

Bravo AF: 0.522

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320561; hg19: chr20-23097880;