1-54162157-A-G

Position:

• chr1-54162157-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 0.855 in 152,236 control chromosomes in the GnomAD database, including 55,688 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 0.85 (55688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 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: 0.855 AC: 130006 AN: 152118 Hom.: 55644 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.855 AC: 130108 AN: 152236 Hom.: 55688 Cov.: 33 AF XY: 0.852 AC XY: 63383 AN XY: 74420

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.858

Alfa AF: 0.884 Hom.: 78189

Bravo AF: 0.854

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs618465; hg19: chr1-54627830;