rs2254907

Variant names:

• chr21-26741351-C-T
• rs2254907

Variant summary

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

The variant allele was found at a frequency of 0.447 in 152,004 control chromosomes in the GnomAD database, including 15,435 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 0.45 (15435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67929 AN: 151886 Hom.: 15427 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.447 AC: 67963 AN: 152004 Hom.: 15435 Cov.: 32 AF XY: 0.444 AC XY: 32974 AN XY: 74306

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.434

Alfa AF: 0.466 Hom.: 17178

Bravo AF: 0.445

Asia WGS AF: 0.365 AC: 1271 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2254907; hg19: chr21-28113670;