chr10-2364437-T-C

Position:

• chr10-2364437-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 0.703 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;