10-53447468-C-G

Position:

• chr10-53447468-C-G

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 0.497 in 152,094 control chromosomes in the GnomAD database, including 19,260 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 0.50 (19260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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: 0.497 AC: 75597 AN: 151976 Hom.: 19256 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.497 AC: 75635 AN: 152094 Hom.: 19260 Cov.: 33 AF XY: 0.504 AC XY: 37512 AN XY: 74364

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.525

Alfa AF: 0.328 Hom.: 794

Bravo AF: 0.496

Asia WGS AF: 0.657 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10740548; hg19: chr10-55207228;