10-120355871-C-T

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 0.763 in 152,156 control chromosomes in the GnomAD database, including 44,679 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 0.76 (44679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

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 (SAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116060 AN: 152040 Hom.: 44630 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.763 AC: 116155 AN: 152156 Hom.: 44679 Cov.: 32 AF XY: 0.764 AC XY: 56859 AN XY: 74392

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.751

Alfa AF: 0.758 Hom.: 8875

Bravo AF: 0.750

Asia WGS AF: 0.817 AC: 2844 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	3.6
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2901228; hg19: chr10-122115383;