rs2822686

Positions:

• chr21-14479779-C-T

Variant summary

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

The XR_007067925.1(LOC124905053):​n.339+2112C>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 0.29 in 152,006 control chromosomes in the GnomAD database, including 8,565 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 0.29 (8565 hom., cov: 31)
• Consequence: LOC124905053 XR_007067925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

LOC124905053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905053	XR_007067925.1	n.339+2112C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44070 AN: 151888 Hom.: 8534 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.290 AC: 44141 AN: 152006 Hom.: 8565 Cov.: 31 AF XY: 0.289 AC XY: 21472 AN XY: 74296

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.261

Alfa AF: 0.211 Hom.: 4108

Bravo AF: 0.295

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822686; hg19: chr21-15852100;