chr10-18125291-C-T

Variant names:

• chr10-18125291-C-T
• rs7897163

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 0.278 in 151,912 control chromosomes in the GnomAD database, including 6,646 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 0.28 (6646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.278 AC: 42127 AN: 151794 Hom.: 6630 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.278 AC: 42184 AN: 151912 Hom.: 6646 Cov.: 32 AF XY: 0.280 AC XY: 20787 AN XY: 74260

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0751

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.260

Alfa AF: 0.219 Hom.: 7890

Bravo AF: 0.281

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.062
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7897163; hg19: chr10-18414220;