chr1-154391509-A-C

Position:

• chr1-154391509-A-C

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 0.284 in 151,972 control chromosomes in the GnomAD database, including 6,247 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 (6247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43209 AN: 151854 Hom.: 6243 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.284 AC: 43235 AN: 151972 Hom.: 6247 Cov.: 31 AF XY: 0.283 AC XY: 21019 AN XY: 74270

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.275

Alfa AF: 0.279 Hom.: 12179

Bravo AF: 0.286

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11582424; hg19: chr1-154363985;