chr10-15929236-A-G

Position:

• chr10-15929236-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.383 in 152,034 control chromosomes in the GnomAD database, including 13,553 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 0.38 (13553 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15929236A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58221 AN: 151918 Hom.: 13546 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.383 AC: 58246 AN: 152034 Hom.: 13553 Cov.: 32 AF XY: 0.398 AC XY: 29603 AN XY: 74334

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.409

Alfa AF: 0.414 Hom.: 8498

Bravo AF: 0.369

Asia WGS AF: 0.723 AC: 2509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010242; hg19: chr10-15971235;