10-26872003-T-C

Variant names:

• chr10-26872003-T-C
• rs2505963

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;