rs2830848

Variant names:

• chr21-27308877-G-A
• rs2830848
• XR_430359.4:n.847+41622C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-27308877-G-A
• chr21-27308877-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_430359.4(LOC102724355):​n.847+41622C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,062 control chromosomes in the GnomAD database, including 8,160 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 (8160 hom., cov: 32)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 0 publications found

Genes affected

LOC102724355 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44798 AN: 151942 Hom.: 8164 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.295 AC: 44784 AN: 152062 Hom.: 8160 Cov.: 32 AF XY: 0.293 AC XY: 21777 AN XY: 74320

African (AFR) AF: 0.0865 AC: 3594 AN: 41530

American (AMR) AF: 0.292 AC: 4452 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1492 AN: 3464

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5154

South Asian (SAS) AF: 0.188 AC: 908 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4380 AN: 10556

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27031 AN: 67970

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.361 Hom.: 17556

Bravo AF: 0.279

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs2830848; hg19: chr21-28681196;