rs2249038

Variant names:

• chr21-24118498-A-C
• rs2249038

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.415 AC: 17190 AN: 41450

American (AMR) AF: 0.0971 AC: 1485 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3472

East Asian (EAS) AF: 0.145 AC: 750 AN: 5176

South Asian (SAS) AF: 0.0542 AC: 262 AN: 4834

European-Finnish (FIN) AF: 0.00744 AC: 79 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0314 AC: 2134 AN: 67992

Other (OTH) AF: 0.123 AC: 261 AN: 2116

Alfa AF: 0.107 Hom.: 364

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2249038; hg19: chr21-25490811;