1-234722850-A-T

Variant names:

• chr1-234722850-A-T
• rs514230

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 67 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.754 AC: 31212 AN: 41410

American (AMR) AF: 0.681 AC: 10402 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3466

East Asian (EAS) AF: 0.766 AC: 3956 AN: 5164

South Asian (SAS) AF: 0.669 AC: 3223 AN: 4816

European-Finnish (FIN) AF: 0.572 AC: 6044 AN: 10562

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35947 AN: 67944

Other (OTH) AF: 0.596 AC: 1258 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs514230; hg19: chr1-234858597;