chr1-19022787-C-T

Variant names:

• chr1-19022787-C-T
• rs28829049
• XR_947015.2:n.552-25728G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_947015.2(LOC105376815):​n.552-25728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 150,808 control chromosomes in the GnomAD database, including 7,860 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 0.30 (7860 hom., cov: 30)
• Consequence: LOC105376815 XR_947015.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 4 publications found

Genes affected

LOC105376815 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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: 0.299 AC: 45043 AN: 150710 Hom.: 7855 Cov.: 30

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.299 AC: 45067 AN: 150808 Hom.: 7860 Cov.: 30 AF XY: 0.304 AC XY: 22411 AN XY: 73600

African (AFR) AF: 0.153 AC: 6259 AN: 40990

American (AMR) AF: 0.422 AC: 6398 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1372 AN: 3456

East Asian (EAS) AF: 0.685 AC: 3512 AN: 5128

South Asian (SAS) AF: 0.310 AC: 1471 AN: 4752

European-Finnish (FIN) AF: 0.316 AC: 3233 AN: 10236

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.321 AC: 21769 AN: 67776

Other (OTH) AF: 0.323 AC: 679 AN: 2100

Alfa AF: 0.309 Hom.: 4001

Bravo AF: 0.303

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	10
DANN	Benign	0.62
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs28829049; hg19: chr1-19349281;