rs2394443

chr10-67884583-G-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 0.599 in 1,031,224 control chromosomes in the GnomAD database, including 196,586 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 0.47 (20786 hom., cov: 34)
  • Exomes 𝑓: 0.62 (175800 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 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: 0.470 AC: 71374 AN: 151954 Hom.: 20790 Cov.: 34

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.505

GnomAD4 exome AF: 0.622 AC: 546511 AN: 879152 Hom.: 175800 AF XY: 0.623 AC XY: 261571 AN XY: 419626

Gnomad4 AFR exome AF: 0.120

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.683

Gnomad4 EAS exome AF: 0.171

Gnomad4 SAS exome AF: 0.442

Gnomad4 FIN exome AF: 0.593

Gnomad4 NFE exome AF: 0.656

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.469 AC: 71363 AN: 152072 Hom.: 20786 Cov.: 34 AF XY: 0.466 AC XY: 34629 AN XY: 74338

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.509

Alfa AF: 0.521 Hom.: 2230

Bravo AF: 0.444

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	9.9
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394443; hg19: chr10-69644341;