rs2254907

Positions:

• chr21-26741351-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.26741351C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;