rs4450871

Variant names:

• chr4-4988571-A-G
• rs4450871
• ENST00000774610.1:n.380A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125893.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928306	NR_125893.1		n.569A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300857	ENST00000774610.1		n.380A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000300857	ENST00000774609.1		n.268-15974A>G		intron	N/A

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

African (AFR) AF: 0.837 AC: 34747 AN: 41508

American (AMR) AF: 0.409 AC: 6249 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2046 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2750 AN: 5162

South Asian (SAS) AF: 0.439 AC: 2119 AN: 4826

European-Finnish (FIN) AF: 0.506 AC: 5344 AN: 10566

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30111 AN: 67988

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.519 Hom.: 9370

Bravo AF: 0.567

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs4450871; hg19: chr4-4990298;