rs1937330

chr10-89094288-T-A

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 0.0629 in 152,286 control chromosomes in the GnomAD database, including 423 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 0.063 (423 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0879 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: 0.0630 AC: 9579 AN: 152168 Hom.: 423 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0629 AC: 9577 AN: 152286 Hom.: 423 Cov.: 31 AF XY: 0.0643 AC XY: 4785 AN XY: 74466

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0693 Hom.: 64

Bravo AF: 0.0579

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937330; hg19: chr10-90854045;