rs2853318

Variant names:

• chr8-97271281-A-T
• rs2853318
• NR_125390.1:n.471+147789T>A

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+147789T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,014 control chromosomes in the GnomAD database, including 4,109 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 0.17 (4109 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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+147789T>A		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: 0.172 AC: 26059 AN: 151896 Hom.: 4107 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0883

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.172 AC: 26086 AN: 152014 Hom.: 4109 Cov.: 32 AF XY: 0.168 AC XY: 12466 AN XY: 74308

African (AFR) AF: 0.422 AC: 17447 AN: 41354

American (AMR) AF: 0.126 AC: 1921 AN: 15282

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

East Asian (EAS) AF: 0.0875 AC: 452 AN: 5164

South Asian (SAS) AF: 0.132 AC: 634 AN: 4820

European-Finnish (FIN) AF: 0.0526 AC: 557 AN: 10596

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

European-Non Finnish (NFE) AF: 0.0670 AC: 4560 AN: 68012

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.128 Hom.: 319

Bravo AF: 0.188

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.77
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2853318; hg19: chr8-98283509;