10-118413126-G-T

Variant names:

• chr10-118413126-G-T
• rs1857269

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 0.389 in 151,868 control chromosomes in the GnomAD database, including 11,847 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 0.39 (11847 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.390 AC: 59119 AN: 151754 Hom.: 11845 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.389 AC: 59147 AN: 151868 Hom.: 11847 Cov.: 31 AF XY: 0.398 AC XY: 29547 AN XY: 74182

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.375

Alfa AF: 0.385 Hom.: 23232

Bravo AF: 0.368

Asia WGS AF: 0.504 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	19
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857269; hg19: chr10-120172638;