rs2289599

Positions:

• chr5-77912325-A-G
• chr5-77912325-A-T

Variant summary

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

The NR_105012.1(LOC101929154):​n.170+27500A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,116 control chromosomes in the GnomAD database, including 48,714 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 0.79 (48714 hom., cov: 31)
• Consequence: LOC101929154 NR_105012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

Genes affected

LOC101929154 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929154	NR_105012.1	n.170+27500A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120633 AN: 151998 Hom.: 48667 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.794 AC: 120740 AN: 152116 Hom.: 48714 Cov.: 31 AF XY: 0.795 AC XY: 59099 AN XY: 74332

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.789

Alfa AF: 0.718 Hom.: 51307

Bravo AF: 0.811

Asia WGS AF: 0.801 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2289599; hg19: chr5-77208149;