10-125447269-T-C

Variant names:

• chr10-125447269-T-C
• rs989507

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 0.743 in 152,042 control chromosomes in the GnomAD database, including 42,603 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 0.74 (42603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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: 0.743 AC: 112946 AN: 151926 Hom.: 42563 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.743 AC: 113040 AN: 152042 Hom.: 42603 Cov.: 31 AF XY: 0.743 AC XY: 55220 AN XY: 74280

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.760

Alfa AF: 0.781 Hom.: 71453

Bravo AF: 0.745

Asia WGS AF: 0.823 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989507; hg19: chr10-127135838;