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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724355	XR_430359.4	n.847+41622C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;