10-60776199-C-T

Variant names:

• chr10-60776199-C-T
• rs2448341

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 0.333 in 151,546 control chromosomes in the GnomAD database, including 8,803 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 0.33 (8803 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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: 0.333 AC: 50478 AN: 151426 Hom.: 8807 Cov.: 29

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.333 AC: 50500 AN: 151546 Hom.: 8803 Cov.: 29 AF XY: 0.334 AC XY: 24703 AN XY: 74032

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.336

Alfa AF: 0.350 Hom.: 15530

Bravo AF: 0.339

Asia WGS AF: 0.453 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2448341; hg19: chr10-62535957;