1-162552026-G-A

Position:

• chr1-162552026-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 0.234 in 151,582 control chromosomes in the GnomAD database, including 4,367 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 0.23 (4367 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.234 AC: 35424 AN: 151488 Hom.: 4357 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35472 AN: 151582 Hom.: 4367 Cov.: 30 AF XY: 0.237 AC XY: 17570 AN XY: 74046

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.264

Alfa AF: 0.227 Hom.: 4042

Bravo AF: 0.239

Asia WGS AF: 0.281 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.053
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10753578; hg19: chr1-162521816;