chr13-21241730-G-A

Variant names:

• chr13-21241730-G-A
• rs17064136

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.226 AC: 9374 AN: 41454

American (AMR) AF: 0.0523 AC: 799 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 314 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4824

European-Finnish (FIN) AF: 0.0655 AC: 693 AN: 10580

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4081 AN: 68016

Other (OTH) AF: 0.0883 AC: 186 AN: 2106

Alfa AF: 0.0788 Hom.: 1537

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
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs17064136; hg19: chr13-21815869;