rs2828099

chr21-23380836-A-G

Variant summary

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

The NR_040254.1(D21S2088E):n.148+3852T>C 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 0.371 in 151,790 control chromosomes in the GnomAD database, including 10,917 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 0.37 (10917 hom., cov: 32)
• Consequence: D21S2088E NR_040254.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

D21S2088E (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
D21S2088E	NR_040254.1	n.148+3852T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
D21S2088E	ENST00000656174.1	n.354-7752T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56275 AN: 151672 Hom.: 10898 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.371 AC: 56327 AN: 151790 Hom.: 10917 Cov.: 32 AF XY: 0.367 AC XY: 27221 AN XY: 74192

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0754

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.373

Alfa AF: 0.376 Hom.: 7358

Bravo AF: 0.372

Asia WGS AF: 0.212 AC: 735 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.9
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2828099; hg19: chr21-24753158;