rs2830840

chr21-27293028-G-Cchr21-27293028-G-A

Variant summary

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

The XR_430359.4(LOC102724355):n.848-28458C>G 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 0.547 in 152,032 control chromosomes in the GnomAD database, including 24,275 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 0.55 (24275 hom., cov: 33)
• Consequence: LOC102724355 XR_430359.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

Genes affected

LOC102724355 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724355	XR_430359.4	n.848-28458C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83116 AN: 151914 Hom.: 24263 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.547 AC: 83151 AN: 152032 Hom.: 24275 Cov.: 33 AF XY: 0.546 AC XY: 40525 AN XY: 74280

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.577

Alfa AF: 0.625 Hom.: 15242

Bravo AF: 0.527

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	4.7
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830840; hg19: chr21-28665347;