1-171754669-C-T

Variant names:

• chr1-171754669-C-T
• rs12120152

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 0.359 in 152,054 control chromosomes in the GnomAD database, including 10,285 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 0.36 (10285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54498 AN: 151936 Hom.: 10256 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.359 AC: 54577 AN: 152054 Hom.: 10285 Cov.: 32 AF XY: 0.355 AC XY: 26402 AN XY: 74314

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.380

Alfa AF: 0.330 Hom.: 1469

Bravo AF: 0.368

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12120152; hg19: chr1-171723809;