NR_125390.1:n.471+148582T>C

Variant names:

• chr8-97270488-A-G
• rs1431891
• NR_125390.1:n.471+148582T>C

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+148582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,144 control chromosomes in the GnomAD database, including 4,374 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 0.18 (4374 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927066	NR_125390.1		n.471+148582T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26751 AN: 152026 Hom.: 4372 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.176 AC: 26780 AN: 152144 Hom.: 4374 Cov.: 32 AF XY: 0.172 AC XY: 12820 AN XY: 74400

African (AFR) AF: 0.436 AC: 18063 AN: 41454

American (AMR) AF: 0.129 AC: 1973 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3470

East Asian (EAS) AF: 0.0874 AC: 453 AN: 5182

South Asian (SAS) AF: 0.132 AC: 637 AN: 4808

European-Finnish (FIN) AF: 0.0528 AC: 560 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0672 AC: 4567 AN: 67998

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.115 Hom.: 734

Bravo AF: 0.193

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1431891; hg19: chr8-98282716;