rs10507321

Positions:

• chr13-23030027-G-A
• chr13-23030027-G-T

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 0.055 in 149,930 control chromosomes in the GnomAD database, including 400 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 0.055 (400 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 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: 0.0547 AC: 8191 AN: 149846 Hom.: 387 Cov.: 30

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0152

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0470

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

GnomAD4 genome AF: 0.0550 AC: 8250 AN: 149930 Hom.: 400 Cov.: 30 AF XY: 0.0544 AC XY: 3970 AN XY: 73006

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0393

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0504

Alfa AF: 0.0314 Hom.: 153

Bravo AF: 0.0594

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.078
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507321; hg19: chr13-23604166;