rs1322331

chr10-101226832-A-Cchr10-101226832-A-T

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 0.495 in 152,472 control chromosomes in the GnomAD database, including 19,304 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 (19228 hom., cov: 32)
  • Exomes 𝑓: 0.46 (76 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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 (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.495 AC: 75068 AN: 151672 Hom.: 19197 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.456 AC: 312 AN: 684 Hom.: 76 Cov.: 0 AF XY: 0.435 AC XY: 154 AN XY: 354

Gnomad4 AFR exome AF: 0.733

Gnomad4 AMR exome AF: 0.231

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.643

Gnomad4 NFE exome AF: 0.444

Gnomad4 OTH exome AF: 0.632

GnomAD4 genome AF: 0.495 AC: 75151 AN: 151788 Hom.: 19228 Cov.: 32 AF XY: 0.487 AC XY: 36143 AN XY: 74166

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.467

Alfa AF: 0.457 Hom.: 19690

Bravo AF: 0.504

Asia WGS AF: 0.430 AC: 1491 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	9.9
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322331; hg19: chr10-102986589;