chr13-104733825-A-G

Variant names:

• chr13-104733825-A-G
• rs10492585

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 0.26 in 152,100 control chromosomes in the GnomAD database, including 12,281 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 0.26 (12281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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: 0.259 AC: 39379 AN: 151982 Hom.: 12235 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.260 AC: 39474 AN: 152100 Hom.: 12281 Cov.: 32 AF XY: 0.255 AC XY: 18970 AN XY: 74372

African (AFR) AF: 0.748 AC: 30991 AN: 41450

American (AMR) AF: 0.152 AC: 2315 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.0726 AC: 375 AN: 5164

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4820

European-Finnish (FIN) AF: 0.0301 AC: 320 AN: 10628

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0507 AC: 3449 AN: 67992

Other (OTH) AF: 0.214 AC: 451 AN: 2108

Alfa AF: 0.117 Hom.: 6501

Bravo AF: 0.285

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.047
DANN	Benign	0.80
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10492585; hg19: chr13-105386176;