rs10507321

Variant names:

• chr13-23030027-G-A
• rs10507321

Your query was ambiguous. Multiple possible variants found:

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

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 0.055 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.131 AC: 5353 AN: 40928

American (AMR) AF: 0.0273 AC: 412 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.0393 AC: 135 AN: 3438

East Asian (EAS) AF: 0.0282 AC: 143 AN: 5074

South Asian (SAS) AF: 0.0156 AC: 74 AN: 4734

European-Finnish (FIN) AF: 0.0264 AC: 260 AN: 9830

Middle Eastern (MID) AF: 0.0278 AC: 8 AN: 288

European-Non Finnish (NFE) AF: 0.0257 AC: 1739 AN: 67548

Other (OTH) AF: 0.0504 AC: 105 AN: 2082

Alfa AF: 0.0369 Hom.: 598

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
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs10507321; hg19: chr13-23604166;