chr13-27298172-A-C

Variant names:

• chr13-27298172-A-C
• rs10507379

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 0.0895 in 152,194 control chromosomes in the GnomAD database, including 885 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 0.089 (885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.122 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: 0.0896 AC: 13625 AN: 152076 Hom.: 885 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0299

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0895 AC: 13620 AN: 152194 Hom.: 885 Cov.: 32 AF XY: 0.0925 AC XY: 6876 AN XY: 74372

African (AFR) AF: 0.0190 AC: 791 AN: 41554

American (AMR) AF: 0.0785 AC: 1200 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0301 AC: 145 AN: 4816

European-Finnish (FIN) AF: 0.230 AC: 2422 AN: 10550

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8446 AN: 68020

Other (OTH) AF: 0.0824 AC: 174 AN: 2112

Alfa AF: 0.0990 Hom.: 515

Bravo AF: 0.0745

Asia WGS AF: 0.0200 AC: 69 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	4.8
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10507379; hg19: chr13-27872309;