rs10883437

Positions:

• chr10-100035604-T-A
• chr10-100035604-T-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 0.423 in 152,034 control chromosomes in the GnomAD database, including 14,731 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 0.42 (14731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.423 AC: 64267 AN: 151916 Hom.: 14696 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.423 AC: 64364 AN: 152034 Hom.: 14731 Cov.: 32 AF XY: 0.413 AC XY: 30712 AN XY: 74306

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.439

Alfa AF: 0.402 Hom.: 1596

Bravo AF: 0.447

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.087

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10883437; hg19: chr10-101795361;