rs2451113

Variant names:

• chr8-97261220-G-A
• rs2451113
• NR_125390.1:n.471+157850C>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+157850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,056 control chromosomes in the GnomAD database, including 3,125 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 (3125 hom., cov: 31)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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+157850C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23548 AN: 151936 Hom.: 3125 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.155 AC: 23569 AN: 152056 Hom.: 3125 Cov.: 31 AF XY: 0.152 AC XY: 11313 AN XY: 74328

African (AFR) AF: 0.358 AC: 14836 AN: 41420

American (AMR) AF: 0.121 AC: 1855 AN: 15290

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

East Asian (EAS) AF: 0.115 AC: 596 AN: 5170

South Asian (SAS) AF: 0.139 AC: 666 AN: 4808

European-Finnish (FIN) AF: 0.0526 AC: 556 AN: 10576

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

European-Non Finnish (NFE) AF: 0.0670 AC: 4555 AN: 68006

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.129 Hom.: 303

Bravo AF: 0.170

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2451113; hg19: chr8-98273448;