rs10507449

Variant names:

• chr13-37291646-T-C
• rs10507449

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 0.0336 in 152,264 control chromosomes in the GnomAD database, including 152 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 0.034 (152 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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: 0.0336 AC: 5107 AN: 152146 Hom.: 151 Cov.: 33

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0424

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0336 AC: 5114 AN: 152264 Hom.: 152 Cov.: 33 AF XY: 0.0348 AC XY: 2593 AN XY: 74464

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0157

Gnomad4 FIN AF: 0.0424

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0257 Hom.: 5

Bravo AF: 0.0370

Asia WGS AF: 0.0850 AC: 297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507449; hg19: chr13-37865783;