chr10-78586629-T-G

Position:

• chr10-78586629-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 0.232 in 152,128 control chromosomes in the GnomAD database, including 7,077 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 0.23 (7077 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

Genes affected

ENSG00000282863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78586629T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282863	ENST00000421324.4	n.114+57815T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35177 AN: 152006 Hom.: 7046 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.232 AC: 35266 AN: 152128 Hom.: 7077 Cov.: 32 AF XY: 0.226 AC XY: 16843 AN XY: 74368

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.200

Alfa AF: 0.172 Hom.: 545

Bravo AF: 0.255

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844429; hg19: chr10-80346386;