chr10-121444843-A-T

Position:

• chr10-121444843-A-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 0.42 in 151,948 control chromosomes in the GnomAD database, including 14,296 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 0.42 (14296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 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: 0.420 AC: 63757 AN: 151830 Hom.: 14284 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.420 AC: 63785 AN: 151948 Hom.: 14296 Cov.: 32 AF XY: 0.419 AC XY: 31082 AN XY: 74264

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.0547

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.437

Alfa AF: 0.440 Hom.: 1896

Bravo AF: 0.421

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.028
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072508; hg19: chr10-123204357;