rs4450871

chr4-4988571-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125893.1(LOC101928306):n.569A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,120 control chromosomes in the GnomAD database, including 26,151 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 0.56 (26151 hom., cov: 33)
• Consequence: LOC101928306 NR_125893.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444

Genes affected

LOC101928306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928306	NR_125893.1	n.569A>G		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84947 AN: 152002 Hom.: 26111 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.559 AC: 85032 AN: 152120 Hom.: 26151 Cov.: 33 AF XY: 0.556 AC XY: 41353 AN XY: 74356

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.548

Alfa AF: 0.522 Hom.: 5702

Bravo AF: 0.567

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4450871; hg19: chr4-4990298;