rs11070098

Variant names:

• chr13-94853008-T-C
• rs11070098
• NR_110754.1:n.257-52456T>C

Variant summary

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

The NR_110754.1(LOC101927284):​n.257-52456T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,128 control chromosomes in the GnomAD database, including 11,246 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 0.36 (11246 hom., cov: 33)
• Consequence: LOC101927284 NR_110754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927284	NR_110754.1	n.257-52456T>C		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55065 AN: 152010 Hom.: 11238 Cov.: 33

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00904

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.362 AC: 55094 AN: 152128 Hom.: 11246 Cov.: 33 AF XY: 0.349 AC XY: 25970 AN XY: 74374

African (AFR) AF: 0.536 AC: 22233 AN: 41500

American (AMR) AF: 0.257 AC: 3928 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3466

East Asian (EAS) AF: 0.00906 AC: 47 AN: 5186

South Asian (SAS) AF: 0.140 AC: 677 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2781 AN: 10578

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23309 AN: 67974

Other (OTH) AF: 0.336 AC: 710 AN: 2112

Alfa AF: 0.348 Hom.: 29552

Bravo AF: 0.372

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11070098; hg19: chr13-95505262;