rs1013005

Positions:

• chr10-78809282-A-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 0.388 in 152,204 control chromosomes in the GnomAD database, including 11,516 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 0.39 (11516 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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: 0.388 AC: 58938 AN: 152086 Hom.: 11496 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.388 AC: 59001 AN: 152204 Hom.: 11516 Cov.: 33 AF XY: 0.387 AC XY: 28823 AN XY: 74412

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.372

Alfa AF: 0.390 Hom.: 2334

Bravo AF: 0.380

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013005; hg19: chr10-80569039;