10-52388284-A-C

Position:

• chr10-52388284-A-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 0.714 in 152,128 control chromosomes in the GnomAD database, including 40,238 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 0.71 (40238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108505 AN: 152010 Hom.: 40169 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.714 AC: 108632 AN: 152128 Hom.: 40238 Cov.: 32 AF XY: 0.711 AC XY: 52892 AN XY: 74360

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.667

Alfa AF: 0.617 Hom.: 3517

Bravo AF: 0.723

Asia WGS AF: 0.837 AC: 2906 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1194670; hg19: chr10-54148044;