chr1-155150307-G-A

Position:

• chr1-155150307-G-A

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 0.898 in 152,232 control chromosomes in the GnomAD database, including 61,526 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 0.90 (61526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.898 AC: 136543 AN: 152114 Hom.: 61476 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.898 AC: 136650 AN: 152232 Hom.: 61526 Cov.: 32 AF XY: 0.895 AC XY: 66632 AN XY: 74436

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.874

Alfa AF: 0.863 Hom.: 71258

Bravo AF: 0.903

Asia WGS AF: 0.907 AC: 3155 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	1.3
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6427184; hg19: chr1-155122783;