rs952146

chr1-154396452-A-G

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 0.386 in 152,040 control chromosomes in the GnomAD database, including 11,510 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 0.39 (11510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.386 AC: 58633 AN: 151920 Hom.: 11483 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.386 AC: 58699 AN: 152040 Hom.: 11510 Cov.: 32 AF XY: 0.385 AC XY: 28619 AN XY: 74312

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.362

Alfa AF: 0.380 Hom.: 17442

Bravo AF: 0.381

Asia WGS AF: 0.294 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.9
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952146; hg19: chr1-154368928;