rs2848519

Variant names:

• chr11-98242451-C-G
• rs2848519

Your query was ambiguous. Multiple possible variants found:

• chr11-98242451-C-G
• chr11-98242451-C-T

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 0.382 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.348 AC: 14442 AN: 41466

American (AMR) AF: 0.337 AC: 5154 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2167 AN: 5164

South Asian (SAS) AF: 0.469 AC: 2264 AN: 4826

European-Finnish (FIN) AF: 0.527 AC: 5558 AN: 10552

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26049 AN: 67978

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.239 Hom.: 564

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2848519; hg19: chr11-98113179;