11-98223945-C-T

Variant names:

• chr11-98223945-C-T
• rs2155907

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 151,794 control chromosomes in the GnomAD database, including 11,251 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 (11251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 57878 AN: 151676 Hom.: 11240 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.382 AC: 57922 AN: 151794 Hom.: 11251 Cov.: 32 AF XY: 0.388 AC XY: 28784 AN XY: 74128

African (AFR) AF: 0.346 AC: 14346 AN: 41416

American (AMR) AF: 0.337 AC: 5146 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3464

East Asian (EAS) AF: 0.418 AC: 2149 AN: 5138

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4816

European-Finnish (FIN) AF: 0.528 AC: 5544 AN: 10498

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.384 AC: 26042 AN: 67896

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.380 Hom.: 6414

Bravo AF: 0.363

Asia WGS AF: 0.439 AC: 1510 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2155907; hg19: chr11-98094673;