rs13391794

Positions:

• chr2-98748116-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007087150.1(LOC107985922):​n.416-3204C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,228 control chromosomes in the GnomAD database, including 2,837 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 0.19 (2837 hom., cov: 32)
• Consequence: LOC107985922 XR_007087150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

LOC107985922 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985922	XR_007087150.1	n.416-3204C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28271 AN: 152108 Hom.: 2835 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.186 AC: 28284 AN: 152228 Hom.: 2837 Cov.: 32 AF XY: 0.184 AC XY: 13660 AN XY: 74418

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.0897

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.186

Alfa AF: 0.174 Hom.: 275

Bravo AF: 0.197

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13391794; hg19: chr2-99364579;