10-25737856-T-C

Variant names:

• chr10-25737856-T-C
• rs2263000

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 0.705 in 152,148 control chromosomes in the GnomAD database, including 37,877 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 0.71 (37877 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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: 0.705 AC: 107203 AN: 152030 Hom.: 37851 Cov.: 34

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.705 AC: 107281 AN: 152148 Hom.: 37877 Cov.: 34 AF XY: 0.702 AC XY: 52213 AN XY: 74360

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.725

Alfa AF: 0.713 Hom.: 41630

Bravo AF: 0.709

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2263000; hg19: chr10-26026785;