10-121677436-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 0.8 in 152,028 control chromosomes in the GnomAD database, including 49,130 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 0.80 (49130 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 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: 0.800 AC: 121525 AN: 151910 Hom.: 49075 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.800 AC: 121644 AN: 152028 Hom.: 49130 Cov.: 31 AF XY: 0.805 AC XY: 59793 AN XY: 74312

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.808

Alfa AF: 0.827 Hom.: 14661

Bravo AF: 0.786

Asia WGS AF: 0.860 AC: 2987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1696803; hg19: chr10-123436950;