10-52879340-T-C

Position:

• chr10-52879340-T-C

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 0.313 in 152,124 control chromosomes in the GnomAD database, including 7,565 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 0.31 (7565 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52879340T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47643 AN: 152006 Hom.: 7561 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.313 AC: 47670 AN: 152124 Hom.: 7565 Cov.: 33 AF XY: 0.312 AC XY: 23181 AN XY: 74376

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.323

Alfa AF: 0.247 Hom.: 819

Bravo AF: 0.313

Asia WGS AF: 0.303 AC: 1054 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	3.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11003238; hg19: chr10-54639100;