10-89197646-G-T

Position:

• chr10-89197646-G-T

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 0.274 in 151,064 control chromosomes in the GnomAD database, including 7,462 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 0.27 (7462 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.89197646G>T		intergenic_region
LOC105378418	XR_946180.4	n.355+2938G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41292 AN: 150966 Hom.: 7433 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.274 AC: 41373 AN: 151064 Hom.: 7462 Cov.: 30 AF XY: 0.282 AC XY: 20806 AN XY: 73710

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.256

Alfa AF: 0.166 Hom.: 5656

Bravo AF: 0.285

Asia WGS AF: 0.507 AC: 1759 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	0.41
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7091822; hg19: chr10-90957403;