10-120163187-T-C

Position:

• chr10-120163187-T-C

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 0.376 in 152,072 control chromosomes in the GnomAD database, including 11,879 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 0.38 (11879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57187 AN: 151954 Hom.: 11868 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.376 AC: 57232 AN: 152072 Hom.: 11879 Cov.: 32 AF XY: 0.371 AC XY: 27568 AN XY: 74342

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.333

Alfa AF: 0.326 Hom.: 11132

Bravo AF: 0.385

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7907490; hg19: chr10-121922699;