10-26872003-T-C

Position:

• chr10-26872003-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 0.445 in 152,086 control chromosomes in the GnomAD database, including 17,755 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 0.44 (17755 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26872003T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67643 AN: 151968 Hom.: 17762 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.445 AC: 67630 AN: 152086 Hom.: 17755 Cov.: 31 AF XY: 0.442 AC XY: 32871 AN XY: 74332

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.470

Alfa AF: 0.571 Hom.: 42048

Bravo AF: 0.431

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505963; hg19: chr10-27160932;