10-57512004-T-C

Position:

• chr10-57512004-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 0.511 in 151,988 control chromosomes in the GnomAD database, including 20,136 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 0.51 (20136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77564 AN: 151870 Hom.: 20135 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.511 AC: 77598 AN: 151988 Hom.: 20136 Cov.: 32 AF XY: 0.512 AC XY: 38055 AN XY: 74272

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.498

Alfa AF: 0.495 Hom.: 2942

Bravo AF: 0.517

Asia WGS AF: 0.531 AC: 1843 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2393352; hg19: chr10-59271764;