1-19874497-A-G

Variant names:

• chr1-19874497-A-G
• rs4654903
• XR_947027.3:n.42-8745T>C

Variant summary

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

The XR_947027.3(LOC105376823):​n.42-8745T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,952 control chromosomes in the GnomAD database, including 21,380 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 0.52 (21380 hom., cov: 31)
• Consequence: LOC105376823 XR_947027.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 18 publications found

Genes affected

LOC105376823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79297 AN: 151832 Hom.: 21334 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.523 AC: 79408 AN: 151952 Hom.: 21380 Cov.: 31 AF XY: 0.520 AC XY: 38589 AN XY: 74276

African (AFR) AF: 0.633 AC: 26243 AN: 41452

American (AMR) AF: 0.514 AC: 7848 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1397 AN: 5166

South Asian (SAS) AF: 0.340 AC: 1631 AN: 4804

European-Finnish (FIN) AF: 0.511 AC: 5395 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33829 AN: 67920

Other (OTH) AF: 0.498 AC: 1053 AN: 2114

Alfa AF: 0.495 Hom.: 79302

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.32
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4654903; hg19: chr1-20200990;