rs2823324

chr21-15523514-G-Tchr21-15523514-G-A

Variant summary

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

The XR_001754972.2(LOC105369302):n.3566C>A 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 0.13 in 152,160 control chromosomes in the GnomAD database, including 3,218 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 0.13 (3217 hom., cov: 32)
  • Exomes 𝑓: 0.031 (1 hom.)
• Consequence: LOC105369302 XR_001754972.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

Genes affected

LOC105369302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369302	XR_001754972.2	n.3566C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634644.1	n.355-9580C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19703 AN: 151944 Hom.: 3197 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.101

GnomAD4 exome AF: 0.0306 AC: 3 AN: 98 Hom.: 1 Cov.: 0 AF XY: 0.0256 AC XY: 2 AN XY: 78

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0233

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.130 AC: 19780 AN: 152062 Hom.: 3217 Cov.: 32 AF XY: 0.127 AC XY: 9443 AN XY: 74362

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.00650

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0303 Hom.: 432

Bravo AF: 0.147

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.21
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823324; hg19: chr21-16895833;