chr10-44387113-C-G

Position:

• chr10-44387113-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 0.78 in 152,182 control chromosomes in the GnomAD database, including 46,934 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 0.78 (46934 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.858 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: 0.780 AC: 118596 AN: 152064 Hom.: 46905 Cov.: 34

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.780 AC: 118675 AN: 152182 Hom.: 46934 Cov.: 34 AF XY: 0.786 AC XY: 58496 AN XY: 74438

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.824

Alfa AF: 0.801 Hom.: 6113

Bravo AF: 0.772

Asia WGS AF: 0.772 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413519; hg19: chr10-44882561;