rs229109

Positions:

• chr21-26868255-C-T

Variant summary

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

The XR_937632.3(LOC105372760):​n.323+13039C>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 0.319 in 151,992 control chromosomes in the GnomAD database, including 8,150 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 0.32 (8150 hom., cov: 31)
• Consequence: LOC105372760 XR_937632.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

LOC105372760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372760	XR_937632.3	n.323+13039C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48452 AN: 151872 Hom.: 8143 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.319 AC: 48486 AN: 151992 Hom.: 8150 Cov.: 31 AF XY: 0.310 AC XY: 23041 AN XY: 74318

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.290

Alfa AF: 0.332 Hom.: 1065

Bravo AF: 0.324

Asia WGS AF: 0.205 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
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: rs229109; hg19: chr21-28240574;