rs1321413

Variant names:

• chr20-61137005-C-T
• rs1321413

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 0.319 in 152,060 control chromosomes in the GnomAD database, including 9,421 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 0.32 (9421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

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 (NFE) allele frequency at 95% confidence interval = 0.44 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: 0.320 AC: 48579 AN: 151942 Hom.: 9422 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.319 AC: 48583 AN: 152060 Hom.: 9421 Cov.: 32 AF XY: 0.317 AC XY: 23555 AN XY: 74342

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.329

Alfa AF: 0.411 Hom.: 18331

Bravo AF: 0.303

Asia WGS AF: 0.162 AC: 565 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	2.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321413; hg19: chr20-59712061;