NR_125390.1:n.471+152347A>T

Variant names:

• chr8-97266723-T-A
• rs2053480
• NR_125390.1:n.471+152347A>T

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+152347A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,124 control chromosomes in the GnomAD database, including 2,793 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 0.15 (2793 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+152347A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22486 AN: 152006 Hom.: 2798 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.148 AC: 22493 AN: 152124 Hom.: 2793 Cov.: 32 AF XY: 0.145 AC XY: 10767 AN XY: 74372

African (AFR) AF: 0.339 AC: 14079 AN: 41482

American (AMR) AF: 0.113 AC: 1733 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.0872 AC: 451 AN: 5170

South Asian (SAS) AF: 0.131 AC: 633 AN: 4820

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0668 AC: 4543 AN: 67972

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.0307 Hom.: 25

Bravo AF: 0.162

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.15
DANN	Benign	0.42
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2053480; hg19: chr8-98278951;