1-146016963-C-T

Variant names:

• chr1-146016963-C-T
• rs1535921

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 0.284 in 152,042 control chromosomes in the GnomAD database, including 7,030 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 0.28 (7030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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: 0.284 AC: 43222 AN: 151924 Hom.: 7031 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.284 AC: 43233 AN: 152042 Hom.: 7030 Cov.: 31 AF XY: 0.282 AC XY: 20957 AN XY: 74324

African (AFR) AF: 0.137 AC: 5669 AN: 41508

American (AMR) AF: 0.332 AC: 5076 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3468

East Asian (EAS) AF: 0.166 AC: 859 AN: 5166

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4822

European-Finnish (FIN) AF: 0.358 AC: 3783 AN: 10554

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24488 AN: 67940

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.218 Hom.: 639

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1535921; hg19: chr1-145418050;