rs2838393

Positions:

• chr21-43813437-G-C
• chr21-43813437-G-A

Variant summary

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

The XR_007067897.1(LOC124905033):​n.766G>C 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 0.284 in 151,814 control chromosomes in the GnomAD database, including 6,927 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 (6927 hom., cov: 32)
• Consequence: LOC124905033 XR_007067897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

Genes affected

LOC124905033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905033	XR_007067897.1	n.766G>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43029 AN: 151698 Hom.: 6908 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.284 AC: 43085 AN: 151814 Hom.: 6927 Cov.: 32 AF XY: 0.287 AC XY: 21334 AN XY: 74216

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.278

Alfa AF: 0.243 Hom.: 651

Bravo AF: 0.297

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838393; hg19: chr21-45233318;