1-234722850-A-T

Position:

• chr1-234722850-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 0.622 in 151,948 control chromosomes in the GnomAD database, including 30,208 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 0.62 (30208 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.234722850A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94448 AN: 151830 Hom.: 30168 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.622 AC: 94552 AN: 151948 Hom.: 30208 Cov.: 31 AF XY: 0.625 AC XY: 46390 AN XY: 74252

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.596

Alfa AF: 0.551 Hom.: 13064

Bravo AF: 0.636

Asia WGS AF: 0.714 AC: 2483 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	0.50
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs514230; hg19: chr1-234858597;