10-84260944-T-C

Position:

• chr10-84260944-T-C

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 0.471 in 152,156 control chromosomes in the GnomAD database, including 18,854 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 0.47 (18854 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84260944T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71594 AN: 152038 Hom.: 18827 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.471 AC: 71656 AN: 152156 Hom.: 18854 Cov.: 33 AF XY: 0.472 AC XY: 35078 AN XY: 74368

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.430

Alfa AF: 0.371 Hom.: 15806

Bravo AF: 0.480

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4244950; hg19: chr10-86020700;