13-94811138-C-T

Variant names:

• chr13-94811138-C-T
• rs9302001
• NR_110754.1:n.256+46587C>T

Variant summary

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

The NR_110754.1(LOC101927284):​n.256+46587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,042 control chromosomes in the GnomAD database, including 7,594 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 0.31 (7594 hom., cov: 32)
• Consequence: LOC101927284 NR_110754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 21 publications found

Genes affected

LOC101927284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110754.1. 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
	LOC101927284	NR_110754.1		n.256+46587C>T		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: 0.308 AC: 46724 AN: 151924 Hom.: 7595 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.307 AC: 46742 AN: 152042 Hom.: 7594 Cov.: 32 AF XY: 0.309 AC XY: 22985 AN XY: 74312

African (AFR) AF: 0.221 AC: 9169 AN: 41484

American (AMR) AF: 0.266 AC: 4056 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1854 AN: 5150

South Asian (SAS) AF: 0.501 AC: 2411 AN: 4810

European-Finnish (FIN) AF: 0.361 AC: 3815 AN: 10566

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23427 AN: 67966

Other (OTH) AF: 0.307 AC: 648 AN: 2114

Alfa AF: 0.325 Hom.: 29556

Bravo AF: 0.295

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9302001; hg19: chr13-95463392;