10-121454963-T-G

Variant names:

• chr10-121454963-T-G
• rs11199974

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.382 in 152,062 control chromosomes in the GnomAD database, including 12,446 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 (12446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58148 AN: 151944 Hom.: 12441 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.382 AC: 58161 AN: 152062 Hom.: 12446 Cov.: 32 AF XY: 0.378 AC XY: 28081 AN XY: 74340

African (AFR) AF: 0.235 AC: 9742 AN: 41482

American (AMR) AF: 0.437 AC: 6677 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5172

South Asian (SAS) AF: 0.201 AC: 966 AN: 4816

European-Finnish (FIN) AF: 0.470 AC: 4970 AN: 10566

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32821 AN: 67966

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.297 Hom.: 1058

Bravo AF: 0.377

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs11199974; hg19: chr10-123214477;