13-21241730-G-A

Position:

• chr13-21241730-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 0.104 in 152,122 control chromosomes in the GnomAD database, including 1,296 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 0.10 (1296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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: 0.104 AC: 15805 AN: 152004 Hom.: 1297 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.104 AC: 15821 AN: 152122 Hom.: 1296 Cov.: 32 AF XY: 0.103 AC XY: 7625 AN XY: 74374

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.0883

Alfa AF: 0.0643 Hom.: 507

Bravo AF: 0.108

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17064136; hg19: chr13-21815869;