rs2853312

Variant names:

• chr8-97269091-T-C
• rs2853312
• NR_125390.1:n.471+149979A>G

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+149979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,182 control chromosomes in the GnomAD database, including 3,182 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 0.16 (3182 hom., cov: 31)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 2 publications found

Genes affected

LOC101927066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125390.1. 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
	LOC101927066	NR_125390.1		n.471+149979A>G		intron	N/A

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: 0.156 AC: 23672 AN: 152064 Hom.: 3184 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0885

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.156 AC: 23690 AN: 152182 Hom.: 3182 Cov.: 31 AF XY: 0.153 AC XY: 11374 AN XY: 74416

African (AFR) AF: 0.365 AC: 15153 AN: 41492

American (AMR) AF: 0.118 AC: 1806 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3468

East Asian (EAS) AF: 0.0877 AC: 454 AN: 5174

South Asian (SAS) AF: 0.131 AC: 632 AN: 4820

European-Finnish (FIN) AF: 0.0525 AC: 557 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0673 AC: 4574 AN: 67996

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.131 Hom.: 405

Bravo AF: 0.171

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.69
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2853312; hg19: chr8-98281319;