rs10507380

Variant names:

• chr13-27305389-A-G
• rs10507380

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 0.0886 in 152,076 control chromosomes in the GnomAD database, including 866 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 (866 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0887 AC: 13475 AN: 151958 Hom.: 866 Cov.: 31

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0830

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

GnomAD4 genome AF: 0.0886 AC: 13471 AN: 152076 Hom.: 866 Cov.: 31 AF XY: 0.0916 AC XY: 6808 AN XY: 74322

African (AFR) AF: 0.0181 AC: 753 AN: 41520

American (AMR) AF: 0.0753 AC: 1150 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2424 AN: 10528

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8408 AN: 67980

Other (OTH) AF: 0.0817 AC: 172 AN: 2106

Alfa AF: 0.104 Hom.: 2291

Bravo AF: 0.0733

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.34
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10507380; hg19: chr13-27879526;