1-182572946-G-T

Position:

• chr1-182572946-G-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 0.456 in 151,952 control chromosomes in the GnomAD database, including 16,298 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 0.46 (16298 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 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: 0.456 AC: 69208 AN: 151834 Hom.: 16292 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.456 AC: 69227 AN: 151952 Hom.: 16298 Cov.: 31 AF XY: 0.457 AC XY: 33937 AN XY: 74278

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.454

Alfa AF: 0.469 Hom.: 6831

Bravo AF: 0.431

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
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: rs627839; hg19: chr1-182542081;