chr1-234722850-A-T

Variant names:

• chr1-234722850-A-T
• rs514230

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;