chr1-228862088-T-G

Position:

• chr1-228862088-T-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 0.474 in 152,018 control chromosomes in the GnomAD database, including 19,602 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 0.47 (19602 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.228862088T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72020 AN: 151900 Hom.: 19553 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.474 AC: 72118 AN: 152018 Hom.: 19602 Cov.: 32 AF XY: 0.471 AC XY: 34999 AN XY: 74292

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.484

Alfa AF: 0.378 Hom.: 24559

Bravo AF: 0.498

Asia WGS AF: 0.386 AC: 1343 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	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs801114; hg19: chr1-228997835;