rs11883722

chr2-203936122-G-A

Variant summary

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

The XR_427213.4(LOC101927840):n.394C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,768 control chromosomes in the GnomAD database, including 7,011 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 0.28 (7011 hom., cov: 31)
• Consequence: LOC101927840 XR_427213.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

LOC101927840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927840	XR_427213.4	n.394C>T		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42615 AN: 151654 Hom.: 6987 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.281 AC: 42684 AN: 151768 Hom.: 7011 Cov.: 31 AF XY: 0.279 AC XY: 20670 AN XY: 74158

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.278

Alfa AF: 0.227 Hom.: 3866

Bravo AF: 0.295

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11883722; hg19: chr2-204800845;