11-98254676-A-G

Variant names:

• chr11-98254676-A-G
• rs2509843

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 0.377 in 151,932 control chromosomes in the GnomAD database, including 11,043 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 (11043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 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: 0.377 AC: 57298 AN: 151816 Hom.: 11034 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.377 AC: 57340 AN: 151932 Hom.: 11043 Cov.: 32 AF XY: 0.384 AC XY: 28530 AN XY: 74244

African (AFR) AF: 0.333 AC: 13777 AN: 41434

American (AMR) AF: 0.337 AC: 5144 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3464

East Asian (EAS) AF: 0.421 AC: 2163 AN: 5142

South Asian (SAS) AF: 0.466 AC: 2250 AN: 4826

European-Finnish (FIN) AF: 0.528 AC: 5558 AN: 10522

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26021 AN: 67948

Other (OTH) AF: 0.379 AC: 800 AN: 2110

Alfa AF: 0.379 Hom.: 8981

Bravo AF: 0.359

Asia WGS AF: 0.440 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.62
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2509843; hg19: chr11-98125404;