chr1-154308146-C-T

Position:

• chr1-154308146-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 0.529 in 151,944 control chromosomes in the GnomAD database, including 21,647 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 0.53 (21647 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.528 AC: 80237 AN: 151826 Hom.: 21619 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.529 AC: 80310 AN: 151944 Hom.: 21647 Cov.: 31 AF XY: 0.529 AC XY: 39316 AN XY: 74270

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.502

Alfa AF: 0.511 Hom.: 7796

Bravo AF: 0.520

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4103781; hg19: chr1-154280622;