rs2249038

Positions:

• chr21-24118498-A-C

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 0.146 in 152,152 control chromosomes in the GnomAD database, including 3,783 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 0.15 (3783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22237 AN: 152034 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0542

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.146 AC: 22284 AN: 152152 Hom.: 3783 Cov.: 32 AF XY: 0.143 AC XY: 10673 AN XY: 74404

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0542

Gnomad4 FIN AF: 0.00744

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0942 Hom.: 300

Bravo AF: 0.166

Asia WGS AF: 0.105 AC: 363 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249038; hg19: chr21-25490811;