11-98242451-C-G

Variant names:

• chr11-98242451-C-G
• rs2848519

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 0.382 in 152,054 control chromosomes in the GnomAD database, including 11,285 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 0.38 (11285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 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: 0.382 AC: 58026 AN: 151934 Hom.: 11274 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.382 AC: 58071 AN: 152054 Hom.: 11285 Cov.: 32 AF XY: 0.389 AC XY: 28890 AN XY: 74336

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.381

Alfa AF: 0.239 Hom.: 564

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2848519; hg19: chr11-98113179;