chr1-171754669-C-T

Position:

• chr1-171754669-C-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 0.359 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;