chr1-152054539-A-T

Position:

• chr1-152054539-A-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 0.145 in 152,248 control chromosomes in the GnomAD database, including 2,245 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 0.15 (2245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.146 AC: 22155 AN: 152130 Hom.: 2243 Cov.: 32

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.145 AC: 22147 AN: 152248 Hom.: 2245 Cov.: 32 AF XY: 0.147 AC XY: 10927 AN XY: 74438

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.148

Alfa AF: 0.190 Hom.: 397

Bravo AF: 0.125

Asia WGS AF: 0.0590 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12130862; hg19: chr1-152027015;