10-2364437-T-C

Variant names:

• chr10-2364437-T-C
• rs826472

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 0.703 in 152,044 control chromosomes in the GnomAD database, including 38,521 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 0.70 (38521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.703 AC: 106852 AN: 151924 Hom.: 38469 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.703 AC: 106958 AN: 152044 Hom.: 38521 Cov.: 33 AF XY: 0.706 AC XY: 52442 AN XY: 74324

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.671

Alfa AF: 0.645 Hom.: 10298

Bravo AF: 0.712

Asia WGS AF: 0.736 AC: 2555 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826472; hg19: chr10-2406631;