rs1320561

Variant names:

• chr20-23117243-G-A
• rs1320561

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;